Evolution of the repression mechanisms in circadian clocks

Background Circadian (daily) timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative feedback between an activator and repressor. However, the role of this feedback varies widely between lower and higher organisms. Results Here, we study repression mechanisms in the cyanobacterial and eukaryotic clocks through mathematical modeling and systems analysis. We find a common mathematical model that describes the mechanism by which organisms generate rhythms; however, transcription’s role in this has diverged. In cyanobacteria, protein sequestration and phosphorylation generate and regulate rhythms while transcription regulation keeps proteins in proper stoichiometric balance. Based on recent experimental work, we propose a repressor phospholock mechanism that models the negative feedback through transcription in clocks of higher organisms. Interestingly, this model, when coupled with activator phosphorylation, allows for oscillations over a wide range of protein stoichiometries, thereby reconciling the negative feedback mechanism in Neurospora with that in mammals and cyanobacteria. Conclusions Taken together, these results paint a picture of how circadian timekeeping may have evolved.

Experiments in artificial culture: from noisy imitation to storytelling robots

This paper presents a series of experiments in collective social robotics, spanning more than 10 years, with the long-term aim of building embodied models of (aspects of) cultural evolution. Initial experiments demonstrated the emergence of behavioural traditions in a group of social robots programmed to imitate each other’s behaviours (we call these Copybots). These experiments show that the noisy (i.e. less than perfect fidelity) imitation that comes for free with real physical robots gives rise naturally to variation in social learning. More recent experimental work extends the robots’ cognitive capabilities with simulation-based internal models, equipping them with a simple artificial theory of mind. With this extended capability we explore, in our current work, social learning not via imitation but robot–robot storytelling, in an effort to model this very human mode of cultural transmission. In this paper, we give an account of the methods and inspiration for these experiments, the experiments and their results, and an outline of possible directions for this programme of research. It is our hope that this paper stimulates not only discussion but suggestions for hypotheses to test with the Storybots. This article is part of a discussion meeting issue ‘The emergence of collective knowledge and cumulative culture in animals, humans and machines’.

Effects of Cholesterol on the mechanism of fengycin, a biofungicide

Fengycins are a class of antifungal lipopeptides synthesized by the bacteria Bacillus subtilis, commercially available as the primary component of the agricultural fungicide Serenade. They are toxic to fungi, but far less to mammalian cells. One key difference between mammalian and fungal cell membranes is the presence of cholesterol only in the former; recent experimental work showed that the presence of cholesterol reduces fengycin-induced membrane leakage. Since our previous all-atom and coarse-grained simulations suggested that aggregation of membrane-bound fengycin is central to its ability to disrupt membranes, we hypothesized that cholesterol might reduce fengycin aggregation. Here, we test this hypothesis using coarse-grained molecular dynamics simulations, with sampling enhanced via the weighted ensemble method. The results indicate that cholesterol subtly alters the size distribution for fengycin aggregates, limits the lateral range of their membrane disordering, and reduces the ability of aggregates to bend the membrane. Taken together, these phenomena may account for cholesterols' affects on fengycin activity.

High Temperature Hydrogen Attack (HTHA) Models for the Petrochemical Industry

Establishing safe operating limits for equipment operating in hydrogen service remains a concern for the petrochemical industry. A methodology to prioritize equipment, inform future inspections, and guide inspection discovery path forward decisions has been in development for the past several years. The approach is multi-tiered and considers the process conditions that lead to risk of damage, the potential extent of damage, and the effect of applied and residual stresses on the rate of damage growth. The key metric for Fe-C steels and Fe-C-0.5Mo steels is the damage index, which is calculated from a damage rate equation that has been calibrated to select laboratory test data and reported HTHA incidents documented in API 941. The damage rate and significance of damage is handled by considering damage as both diffuse (continuum assessment) and localized (crack/flaw assessment). This approach was originally intended as a means for prioritizing inspection. However, once margins are established to account for uncertainties in operating conditions and material variation, so-called time-dependent Nelson curves can be generated for use in design. This paper provides an overview of the HTHA damage modeling technique and results of recent experimental work, including component-level testing used for validation of the model.

Number in the Mental Lexicon

This chapter discusses the representation and processing of grammatical number in language comprehension and production. Grammatical number is regarded as a syntactic feature stored with a word's lemma, i.e. the syntactic word, in the mental lexicon. The chapter discusses the representation of grammatical number in the mental lexicon and how this feature is selected. Comparisons to other grammatical features, such as grammatical gender, are also made. Moreover, the chapter reviews experimental work both in the area of language comprehension and language production to shed light on the processing of grammatical number in human cognition. The chapter closes with a report on recent experimental work conducted on Konso, a Cushitic language spoken in the south of Ethiopia. In Konso, the number feature interacts with the gender feature. Data from picture-naming experiments demonstrate that so-called plural gender should be interpreted as a gender feature rather than as a number feature.

Let's talk (efficiently) about us: Person systems achieve near-optimal compression

Systems of personal pronouns (e.g., 'you' and 'I') vary widely across languages, but at the same time not all possible systems are attested. Linguistic theories have generally accounted for this in terms of strong grammatical constraints, but recent experimental work challenges this view. Here, we take a novel approach to understanding personal pronoun systems by invoking a recent information-theoretic framework for semantic systems that predicts that languages efficiently compress meanings into forms. We find that a test set of cross-linguistically attested personal pronoun systems achieves near-optimal compression, supporting the hypothesis that efficient compression shapes semantic systems. Further, our best-fitting model includes an egocentric bias that favors a salient speaker representation, accounting for a well-known typological generalization of person systems ('Zwicky's Generalization') without the need for a hard grammatical constraint.

Flipping the switch on the hub cell: Islet desynchronization through cell silencing

Pancreatic β cells, responsible for secreting insulin into the bloodstream and maintaining glucose homeostasis, are organized in the islets of Langerhans as clusters of electrically coupled cells. Gap junctions, connecting neighboring cells, coordinate the behavior of the islet, leading to the synchronized oscillations in the intracellular calcium and insulin secretion in healthy islets. Recent experimental work has shown that silencing special hub cells can lead to a disruption in the coordinated behavior, calling into question the democratic paradigm of islet insulin secretion with more or less equal input from each β cell. Islets were shown to have scale-free functional connectivity and a hub cell whose silencing would lead to a loss of functional connectivity and activity in the islet. A mechanistic model representing the electrical and calcium dynamics of β cells during insulin secretion was applied to a network of cells connected by gap junctions to test the hypothesis of hub cells. Functional connectivity networks were built from the simulated calcium traces, with some networks classified as scale-free, confirming experimental results. Potential hub cells were identified using previously defined centrality measures, but silencing them was unable to desynchronize the islet. Instead, switch cells, which were able to turn off the activity of the islet but were not highly functionally connected, were found via systematically silencing each cell in the network.

Generation of Supra-Wavelength Grooves in Femtosecond Laser Surface Structuring of Silicon

Extensive research work has been carried out on the generation and application of laser-induced periodic surface structures (LIPSS). LIPSS with a sub-wavelength period generated by femtosecond laser irradiation, generally indicated as ripples, have been extensively investigated. Instead, the other ordered surface structures characterized by a supra-wavelength period, indicated as grooves, have been much less studied. Grooves typically form at larger irradiance levels or for higher number of laser pulses. Here, we report a comprehensive overview of recent investigations on the supra-wavelength grooves formed on crystalline silicon irradiated by femtosecond laser pulses. The authors’ recent experimental work is mainly addressed giving an explicit picture of the grooves generation process, namely illustrating the influence of the various experimental parameters, including, e.g., polarization, wavelength, fluence and repetition rate of the laser beam as well as number of laser pulses hitting the surface of the material. The effect of irradiation of a static or moving target and of the environmental conditions (e.g., vacuum or air ambient) will also be discussed. Finally, possible mechanisms envisaged to explain grooves formation and still open issues are briefly discussed.

Recent Advances in the Development of Nano-Sculpted Films by Magnetron Sputtering for Energy-Related Applications

In this paper, we overview the recent progress we made in the magnetron sputtering-based developments of nano-sculpted thin films intended for energy-related applications such as energy conversion. This paper summarizes our recent experimental work often supported by simulation and theoretical results. Specifically, the development of a new generation of nano-sculpted photo-anodes based on TiO2 for application in dye-sensitized solar cells is discussed.

A conceptual framework for the study of demonstrative reference

Language allows us to efficiently communicate about the things in the world around us. Seemingly simple words like this and that are a cornerstone of our capability to refer, as they contribute to guiding the attention of our addressee to the specific entity we are talking about. Such demonstratives are acquired early in life, ubiquitous in everyday talk, often closely tied to our gestural communicative abilities, and present in all spoken languages of the world. Based on a review of recent experimental work, here we introduce a new conceptual framework of demonstrative reference. In the context of this framework, we argue that several physical, psychological, and referent-intrinsic factors dynamically interact to influence whether a speaker will use one demonstrative form (e.g., this) or another (e.g., that) in a given setting. However, the relative influence of these factors themselves is argued to be a function of the cultural language setting at hand, the theory-of-mind capacities of the speaker, and the affordances of the specific context in which the speech event takes place. It is demonstrated that the framework has the potential to reconcile findings in the literature that previously seemed irreconcilable. We show that the framework may to a large extent generalize to instances of endophoric reference (e.g., anaphora) and speculate that it may also describe the specific form and kinematics a speaker’s pointing gesture takes. Testable predictions and novel research questions derived from the framework are presented and discussed.