Natural biological systems are selected by evolution to continue to exist and evolve. Evolution likely gives rise to complicated systems that are difficult to understand and manipulate. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. Our initial design goals were to physically separate and enable unique manipulation of primary genetic elements. Implicit in our design are the hypotheses that overlapping genetic elements are, in aggregate, nonessential for T7 viability and that our models for the functions encoded by elements are sufficient. To test our initial design, we replaced the left 11,515 base pairs (bp) of the 39,937 bp wild-type genome with 12,179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.

In addition to the red terra sigillata production, the largest Gallic workshop (La Graufesenque) made a special type of terra sigillata, called “marbled” by the archaeologists. Produced exclusively at this site, this pottery is characterized by a surface finish made of a mixture of yellow and red slips. Because the two slips are intimately mixed, it is difficult to obtain the precise composition of one of the two constituents without contamination from the other. In order to obtain very precise correlation at the appropriate scale between the color aspect and the elemental and mineralogical phase distributions in the slip, combined electron microprobe, X-ray micro spectroscopies and micro diffraction on cross-sectional samples were performed. The aim of this study is to discover how potters were able to produce this unique type of terra sigillata and especially this particular slip of an intense yellow color. Results show that the yellow component of marbled sigillata was made from a titanium-rich clay preparation. The color is due to the formation of a pseudobrookite (TiFe2O5) phase in the yellow part of the slip, the main characteristics of that structure being considered nowadays as essential for the fabrication of stable yellow ceramic pigments. Its physical properties such as high refractive indices and a melting point higher than that of most silicates widely used as ceramic colorants are indeed determinant for this kind of application. Finally, the red parts have a similar composition (elementary and mineralogical) to the one of standard red slip.

Predictive coding (PC) has been suggested as one of the main mechanisms used by brains to interact with complex environments. PC theories posit top-down prediction signals, which are compared with actual outcomes, yielding in turn prediction error (PE) signals, which are used, bottom-up, to modify the ensuing predictions. However, disentangling prediction from PE signals has been challenging. Critically, while many studies found indirect evidence for PC in the form of PE signals, direct evidence for the prediction signal is mostly lacking. Here, we provide clear evidence, obtained from intracranial cortical recordings in human surgical patients, that the human lateral prefrontal cortex evinces prediction signals while anticipating an event. Patients listened to task-irrelevant sequences of repetitive tones including infrequent predictable or unpredictable pitch deviants. The broadband high-frequency amplitude (HFA) was decreased prior to the onset of expected relative to unexpected deviants in the frontal cortex only, and its amplitude was sensitive to the increasing likelihood of deviants following longer trains of standards in the unpredictable condition. Single-trial HFA predicted deviations and correlated with poststimulus response to deviations. These results provide direct evidence for frontal cortex prediction signals independent of PE signals.

Recent advances in dry electrodes technology have facilitated the recording of EEG in situations not previously possible, thanks to the relatively swift electrode preparation and avoidance of applying gel to subject's hair. However, to become a true alternative, these systems should be compared to state-of-the-art wet EEG systems commonly used in clinical or research applications. In our study, we conducted a systematic comparison of electrodes application speed, subject comfort, and most critically electrophysiological signal quality between the conventional and wired Biosemi EEG system using wet active electrodes and the compact and wireless F1 EEG system consisting of dry passive electrodes. All subjects (n = 27) participated in two recording sessions on separate days, one with the wet EEG system and one with the dry EEG system, in which the session order was counterbalanced across subjects. In each session, we recorded their EEG during separate rest periods with eyes open and closed followed by two versions of a serial visual presentation target detection task. Each task component allows for a neural measure reflecting different characteristics of the data, including spectral power in canonical low frequency bands, event-related potential components (specifically, the P3b), and single trial classification based on machine learning. The performance across the two systems was similar in most measures, including the P3b amplitude and topography, as well as low frequency (theta, alpha, and beta) spectral power at rest. Both EEG systems performed well above chance in the classification analysis, with a marginal advantage of the wet system over the dry. Critically, all aforementioned electrophysiological metrics showed significant positive correlations (r = 0.54-0.89) between the two EEG systems. This multitude of measures provides a comprehensive comparison that captures different aspects of EEG data, including temporal precision, frequency domain as well as multivariate patterns of activity. Taken together, our results indicate that the dry EEG system used in this experiment can effectively record electrophysiological measures commonly used across the research and clinical contexts with comparable quality to the conventional wet EEG system.

Predictive coding theories posit that neural networks learn statistical regularities in the environment for comparison with actual outcomes, signaling a prediction error (PE) when sensory deviation occurs. PE studies in audition have capitalized on low-frequency event-related potentials (LF-ERPs), such as the mismatch negativity. However, local cortical activity is well-indexed by higher-frequency bands [high-γ band (Hγ): 80-150 Hz]. We compared patterns of human Hγ and LF-ERPs in deviance detection using electrocorticographic recordings from subdural electrodes over frontal and temporal cortices. Patients listened to trains of task-irrelevant tones in two conditions differing in the predictability of a deviation from repetitive background stimuli (fully predictable vs. unpredictable deviants). We found deviance-related responses in both frequency bands over lateral temporal and inferior frontal cortex, with an earlier latency for Hγ than for LF-ERPs. Critically, frontal Hγ activity but not LF-ERPs discriminated between fully predictable and unpredictable changes, with frontal cortex sensitive to unpredictable events. The results highlight the role of frontal cortex and Hγ activity in deviance detection and PE generation.

Superficial white matter (SWM) represents a significantly understudied part of the human brain, despite comprising a large portion of brain volume and making up a majority of cortico-cortical white matter connections. Using multiple, high-quality datasets with large sample sizes (N = 2421, age range 5-100) in combination with methodological advances in tractography, we quantified features of SWM volume and thickness across the brain and across development, young adulthood, and aging. We had four primary aims: (1) characterize SWM thickness across brain regions (2) describe associations between SWM volume and age (3) describe associations between SWM thickness and age, and (4) quantify relationships between SWM thickness and cortical features. Our main findings are that (1) SWM thickness varies across the brain, with patterns robust across individuals and across the population at the region-level and vertex-level; (2) SWM volume shows unique volumetric trajectories with age that are distinct from gray matter and other white matter trajectories; (3) SWM thickness shows nonlinear cross-sectional changes across the lifespan that vary across regions; and (4) SWM thickness is associated with features of cortical thickness and curvature. For the first time, we show that SWM volume follows a similar trend as overall white matter volume, peaking at a similar time in adolescence, leveling off throughout adulthood, and decreasing with age thereafter. Notably, the relative fraction of total brain volume of SWM continuously increases with age, and consequently takes up a larger proportion of total white matter volume, unlike the other tissue types that decrease with respect to total brain volume. This study represents the first characterization of SWM features across the large portion of the lifespan and provides the background for characterizing normal aging and insight into the mechanisms associated with SWM development and decline.

We recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference collaborate to down-regulate protein expression. Developmentally timed transcriptional interference inhibited production of a well translated mRNA isoform and resulted in the production of an mRNA isoform containing inhibitory upstream open reading frames (uORFs) that prevented translation of the main ORF. Transcriptional interference and uORF-based translational repression are established mechanisms outside of yeast, but whether this type of integrated regulation was conserved was unknown. Here we find that, indeed, a similar type of regulation occurs at the locus for the human oncogene MDM2 We observe evidence of transcriptional interference between the two MDM2 promoters, which produce a poorly translated distal promoter-derived uORF-containing mRNA isoform and a well-translated proximal promoter-derived transcript. Down-regulation of distal promoter activity markedly up-regulates proximal promoter-driven expression and results in local reduction of histone H3K36 trimethylation. Moreover, we observe that this transcript toggling between the two MDM2 isoforms naturally occurs during human embryonic stem cell differentiation programs.