Total synthesis of Escherichia coli with a recoded genome

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA

Stochastic Resonance Modulates Neural Synchronization within and between Cortical Sources

Neural synchronization is a mechanism whereby functionally specific brain regions establish transient networks for perception, cognition, and action. Direct addition of weak noise (fast random fluctuations) to various neural systems enhances synchronization through the mechanism of stochastic resonance (SR). Moreover, SR also occurs in human perception, cognition, and action. Perception, cognition, and action are closely correlated with, and may depend upon, synchronized oscillations within specialized brain networks. We tested the hypothesis that SR-mediated neural synchronization occurs within and between functionally relevant brain areas and thus could be responsible for behavioral SR. We measured the 40-Hz transient response of the human auditory cortex to brief pure tones. This response arises when the ongoing, random-phase, 40-Hz activity of a group of tuned neurons in the auditory cortex becomes synchronized in response to the onset of an above-threshold sound at its “preferred” frequency. We presented a stream of near-threshold standard sounds in various levels of added broadband noise and measured subjects' 40-Hz response to the standards in a deviant-detection paradigm using high-density EEG. We used independent component analysis and dipole fitting to locate neural sources of the 40-Hz response in bilateral auditory cortex, left posterior cingulate cortex and left superior frontal gyrus. We found that added noise enhanced the 40-Hz response in all these areas. Moreover, added noise also increased the synchronization between these regions in alpha and gamma frequency bands both during and after the 40-Hz response. Our results demonstrate neural SR in several functionally specific brain regions, including areas not traditionally thought to contribute to the auditory 40-Hz transient response. In addition, we demonstrated SR in the synchronization between these brain regions. Thus, both intra- and inter-regional synchronization of neural activity are facilitated by the addition of moderate amounts of random noise. Because the noise levels in the brain fluctuate with arousal system activity, particularly across sleep-wake cycles, optimal neural noise levels, and thus SR, could be involved in optimizing the formation of task-relevant brain networks at several scales under normal conditions

Willpower and Conscious Percept: Volitional Switching in Binocular Rivalry

When dissimilar images are presented to the left and right eyes, awareness switches spontaneously between the two images, such that one of the images is suppressed from awareness while the other is perceptually dominant. For over 170 years, it has been accepted that even though the periods of dominance are subject to attentional processes, we have no inherent control over perceptual switching. Here, we revisit this issue in response to evidence that top-down attention can target perceptually suppressed ‘vision for action’ representations in the dorsal stream. We investigated volitional control over rivalry between apparent motion (AM), drifting (DM) and stationary (ST) grating pairs. Observers demonstrated a remarkable ability to generate intentional switches in the AM and D conditions, but not in the ST condition. Corresponding switches in the pursuit direction of optokinetic nystagmus verified this finding objectively. We showed it is unlikely that intentional perceptual switches were triggered by saccadic eye movements, because their frequency was reduced substantially in the volitional condition and did not change around the time of perceptual switches. Hence, we propose that synergy between dorsal and ventral stream representations provides the missing link in establishing volitional control over rivalrous conscious percepts

Testing Developmental Pathways to Antisocial Personality Problems

This study examined the development of antisocial personality problems (APP) in young adulthood from disruptive behaviors and internalizing problems in childhood and adolescence. Parent ratings of 507 children’s (aged 6–8 years) symptoms of attention deficit hyperactivity disorder, oppositional defiant disorder, and anxiety, were linked to self-ratings of adolescents’ (aged 14–16 years) symptoms of depression, substance use, conduct problems, and somatic problems, to predict self-ratings of APP in young adulthood (age 20–22 years). The findings suggested a hierarchical development of antisocial behavior problems. Despite being positively associated with conduct problems in adolescence, neither internalizing problems nor substance use added to the prediction of APP in young adulthood from conduct problems in adolescence. The developmental pathways to APP in young adulthood did not differ by gender

Preschool Behavioral and Social-Cognitive Problems as Predictors of (Pre)adolescent Disruptive Behavior

This article describes preschool social understanding and difficult behaviors (hot temper, disobedience, bossiness and bullying) as predictors of oppositional defiant disorder (ODD) and aggressive conduct disorder (ACD) in a Dutch population sample of (pre)adolescents (N = 1943), measured at age 10–12 and at age 13–15. ODD and ACD were assessed by the Child Behavior Checklist and the Youth Self-Report, preschool behavior was evaluated by the parental questionnaire ‹How was your child as a preschooler? (age 4–5)’. Adjusted for each other, all difficult preschool behaviors except bullying were associated with adolescent ODD, while only bullying significantly predicted adolescent ACD. Furthermore, the results suggest a qualitative difference between ODD and ACD in terms of the social component of the disorders: poor preschool social understanding was associated with the development of ACD but not of ODD; and poor social understanding interacted with difficult preschool behaviors to predict later ACD but not ODD. The associations did not differ between boys and girls, and were roughly similar for preadolescent (age 10–12) and early adolescent (age 13–15) outcomes. The finding that poor social understanding was implicated in the development of ACD but not in the development of ODD may help to demarcate the individuality of each disorder and offer leads for (differential) treatment strategies

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

Metabolic network reconstructions represent valuable scaffolds for ‘-omics’ data integration and are used to computationally interrogate network properties. However, they do not explicitly account for the synthesis of macromolecules (i.e., proteins and RNA). Here, we present the first genome-scale, fine-grained reconstruction of Escherichia coli's transcriptional and translational machinery, which produces 423 functional gene products in a sequence-specific manner and accounts for all necessary chemical transformations. Legacy data from over 500 publications and three databases were reviewed, and many pathways were considered, including stable RNA maturation and modification, protein complex formation, and iron–sulfur cluster biogenesis. This reconstruction represents the most comprehensive knowledge base for these important cellular functions in E. coli and is unique in its scope. Furthermore, it was converted into a mathematical model and used to: (1) quantitatively integrate gene expression data as reaction constraints and (2) compute functional network states, which were compared to reported experimental data. For example, the model predicted accurately the ribosome production, without any parameterization. Also, in silico rRNA operon deletion suggested that a high RNA polymerase density on the remaining rRNA operons is needed to reproduce the reported experimental ribosome numbers. Moreover, functional protein modules were determined, and many were found to contain gene products from multiple subsystems, highlighting the functional interaction of these proteins. This genome-scale reconstruction of E. coli's transcriptional and translational machinery presents a milestone in systems biology because it will enable quantitative integration of ‘-omics’ datasets and thus the study of the mechanistic principles underlying the genotype–phenotype relationship

The “conscious pilot”—dendritic synchrony moves through the brain to mediate consciousness

Cognitive brain functions including sensory processing and control of behavior are understood as “neurocomputation” in axonal–dendritic synaptic networks of “integrate-and-fire” neurons. Cognitive neurocomputation with consciousness is accompanied by 30- to 90-Hz gamma synchrony electroencephalography (EEG), and non-conscious neurocomputation is not. Gamma synchrony EEG derives largely from neuronal groups linked by dendritic–dendritic gap junctions, forming transient syncytia (“dendritic webs”) in input/integration layers oriented sideways to axonal–dendritic neurocomputational flow. As gap junctions open and close, a gamma-synchronized dendritic web can rapidly change topology and move through the brain as a spatiotemporal envelope performing collective integration and volitional choices correlating with consciousness. The “conscious pilot” is a metaphorical description for a mobile gamma-synchronized dendritic web as vehicle for a conscious agent/pilot which experiences and assumes control of otherwise non-conscious auto-pilot neurocomputation

Intergenerational Transmission of Multiple Problem Behaviors: Prospective Relationships between Mothers and Daughters

Much of the research examining intergenerational continuity of problems from mother to offspring has focused on homotypic continuity (e.g., depression), despite the fact that different types of mental health problems tend to cluster in both adults and children. It remains unclear whether mothers with multiple mental health problems compared to mothers with fewer or no problems are more likely to have daughters with multiple mental health problems during middle childhood (ages 7 to 11). Six waves of maternal and child data from the Pittsburgh Girls Study (n = 2,451) were used to examine the specificity of effects of maternal psychopathology on child adjustment. Child multiple mental health problems comprised disruptive behavior, ADHD symptoms, depressed mood, anxiety symptoms and somatic complaints, while maternal multiple mental health problems consisted of depression, prior conduct problems and somatic complaints. Generalized Estimating Equations (GEE) was used to examine the prospective relationships between mother’s single and multiple mental health problems and their daughter’s single and multiple mental health problems across the elementary school-aged period (ages 7–11 years). The results show that multiple mental health problems in the mothers predicted multiple mental health problems in the daughters even when earlier mental health problem of the daughters, demographic factors, and childrearing practices were controlled. Maternal low parental warmth and harsh punishment independently contributed to the prediction of multiple mental health problems in their daughter, but mediation analyses showed that the contribution of parenting behaviors to the explanation of girls’ mental health problems was small