Lipid vesicles chaperone an encapsulated RNA aptamer.

The organization of molecules into cells is believed to have been critical for the emergence of living systems. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids. However, little is known about how encapsulation would affect the activity and folding of RNA. Here we find that confinement of the malachite green RNA aptamer inside fatty acid vesicles increases binding affinity and locally stabilizes the bound conformation of the RNA. The vesicle effectively 'chaperones' the aptamer, consistent with an excluded volume mechanism due to confinement. Protocellular organization thereby leads to a direct benefit for the RNA. Coupled with previously described mechanisms by which encapsulated RNA aids membrane growth, this effect illustrates how the membrane and RNA might cooperate for mutual benefit. Encapsulation could thus increase RNA fitness and the likelihood that functional sequences would emerge during the origin of life

Graphical representations of graphic frame matroids

A frame matroid M is graphic if there is a graph G with cycle matroid isomorphic to M. In general, if there is one such graph, there will be many. Zaslavsky has shown that frame matroids are precisely those having a representation as a biased graph; this class includes graphic matroids, bicircular matroids, and Dowling geometries. Whitney characterized which graphs have isomorphic cycle matroids, and Matthews characterised which graphs have isomorphic graphic bicircular matroids. In this paper, we give a characterization of which biased graphs give rise to isomorphic graphic frame matroids

RNA catalysis in model protocell vesicles.

We are engaged in a long-term effort to synthesize chemical systems capable of Darwinian evolution, based on the encapsulation of self-replicating nucleic acids in self-replicating membrane vesicles. Here, we address the issue of the compatibility of these two replicating systems. Fatty acids form vesicles that are able to grow and divide, but vesicles composed solely of fatty acids are incompatible with the folding and activity of most ribozymes, because low concentrations of divalent cations (e.g., Mg(2+)) cause fatty acids to precipitate. Furthermore, vesicles that grow and divide must be permeable to the cations and substrates required for internal metabolism. We used a mixture of myristoleic acid and its glycerol monoester to construct vesicles that were Mg(2+)-tolerant and found that Mg(2+) cations can permeate the membrane and equilibrate within a few minutes. In vesicles encapsulating a hammerhead ribozyme, the addition of external Mg(2+) led to the activation and self-cleavage of the ribozyme molecules. Vesicles composed of these amphiphiles grew spontaneously through osmotically driven competition between vesicles, and further modification of the membrane composition allowed growth following mixed micelle addition. Our results show that membranes made from simple amphiphiles can form vesicles that are stable enough to retain encapsulated RNAs in the presence of divalent cations, yet dynamic enough to grow spontaneously and allow the passage of Mg(2+) and mononucleotides without specific macromolecular transporters. This combination of stability and dynamics is critical for building model protocells in the laboratory and may have been important for early cellular evolution

Sleeve gastrectomy improves metabolic syndrome in psychologically stable patients with schizophrenia

A clinical decision report appraising: Archid R, Archid N, Meile T, Hoffman J, Wulff D, Teufel M, Muthig M, Quante M, Konigsrainer A, Lange J. Patients with schizophrenia do not demonstrate worse outcome after sleeve gastrectomy: a short-term cohort study. Obesity Surgery. 2019;29:506-510. https://doi.org/10.1007/s11695-018-3578-0 for a patient with schizophrenia and obesity

The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA.

In the early 'RNA world' stage of life, RNA stored genetic information and catalyzed chemical reactions. However, the RNA world eventually gave rise to the DNA-RNA-protein world, and this transition included the 'genetic takeover' of information storage by DNA. We investigated evolutionary advantages for using DNA as the genetic material. The error rate of replication imposes a fundamental limit on the amount of information that can be stored in the genome, as mutations degrade information. We compared misincorporation rates of RNA and DNA in experimental non-enzymatic polymerization and calculated the lowest possible error rates from a thermodynamic model. Both analyses found that RNA replication was intrinsically error-prone compared to DNA, suggesting that total genomic information could increase after the transition to DNA. Analysis of the transitional RNA/DNA hybrid duplexes showed that copying RNA into DNA had similar fidelity to RNA replication, so information could be maintained during the genetic takeover. However, copying DNA into RNA was very error-prone, suggesting that attempts to return to the RNA world would result in a considerable loss of information. Therefore, the genetic takeover may have been driven by a combination of increased chemical stability, increased genome size and irreversibility

Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes.

BackgroundCharacterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic.ResultsWe find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method.ConclusionUse of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples

What Influences the Relative Proportion of ‘Rigid Rotation’ Versus ‘Non-Rigid Deformation’ in a Bistable Stroboscopic Motion Display

When observers are presented with a bistable stroboscopic display of an object that appears to transform over time in three-dimensional (3D) space, the dominance of one percept over another is influenced both by stimulus parameters and by cognitive factors. Two experiments were designed to reveal which of several manipulated variables influence most strongly which of two responses is more often observed, one being termed ‘Rigid Rotation’ and the other termed ‘Non-rigid Deformation.’ These two responses were clearly distinguished when drawings of a 3D rectangular box were presented stroboscopically in a two-frame animation with precise control over the Interstimulus Interval (ISI). In the first experiment, the relative dominance of the ‘Rigid Rotation’ response was reduced by changing the colour of one surface of the rectangular box in a manner that was inconsistent with the rotation of the box. Similarly, the relative dominance of the ‘Non-rigid Deformation’ response was reduced by changing the colour of one surface of the rectangular box in a manner that was inconsistent with deformation of the box. In the second experiment, the changes in the relative dominance of the competing motion percepts were observed after prolonged viewing of four different adapting stimuli. The adaptation aftereffects were shown to depend more upon the Interstimulus Interval (ISI) of the stroboscopic display of the adapting stimulus than upon what motion was reportedly ‘seen’ during the viewing of the adapting stimulus. Ultimately, the adaption aftereffect revealed that the relative dominance of the two movement percepts was affected most strongly by the manipulation of a single temporal variable – the ISI. Nonetheless, the results of the first experiment confirmed the influence of surface colour variations on ‘Rigid Rotation’ versus ‘Non-rigid Deformation’ response

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds.

Chronic wounds represent a large and growing disease burden. Infection and biofilm formation are two of the leading impediments of wound healing, suggesting an important role for the microbiome of these wounds. Debridement is a common and effective treatment for chronic wounds. We analyzed the bacterial content of the wound surface from 20 outpatients with chronic wounds before and immediately after debridement, as well as healthy skin. Given the large variation observed among different wounds, we introduce a Bayesian statistical method that models patient-to-patient variability and identify several genera that were significantly enriched in wounds vs. healthy skin. We found no difference between the microbiome of the original wound surface and that exposed by a single episode of sharp debridement, suggesting that this debridement did not directly alter the wound microbiome. However, we found that aerobes and especially facultative anaerobes were significantly associated with wounds that did not heal within 6 months. The facultative anaerobic genus Enterobacter was significantly associated with lack of healing. The results suggest that an abundance of facultative anaerobes is a negative prognostic factor in the chronic wound microbiome, possibly due to the increased robustness of such communities to different metabolic environments

EFL learners developing critical intercultural awareness through process drama: Dialogue and discovery

Abstract The overall aim of this research study is to look for a paradigm shift in foreign language (English) education in Taiwan. By challenging the role of foreign languages teaching and learning in the reproductive purpose of education systems, this study addresses the significance and urgency of developing critical intercultural awareness (CIA) in Taiwan students’ language learning experience. This study is a reflective account of an action research project that explores the how and why CIA can be developed in process drama praxis in the context of the Advanced English Learners’ Programmes for 27 junior high school students in Taiwan. Drawing on the theoretical framework of socio-cultural and educational drama theories for foreign language learning, this study follows the line of performative inquiry (Fels, 1999; 2000; 2008). As such, the drama site is regarded as a space for reflective action to take place, the drama workshop is seen as a collective experience of reflection, in which the participants are made able to problematise the current situation, to see things from different and distanced perspectives, and develop understanding in every moment of encountering with others, while co-constructing meanings together through dialogue and critical reflections. The narrative accounts of this inquiry serve to answer the major research question: How would a process drama syllabus help EFL learners develop critical intercultural awareness? The qualitative data demonstrated how such the multilayered mental space in drama allowed the language learners to develop flexibility and mobility through a freedom in the choice of action endowed upon them by the drama syllabus. The analysis revealed how drama created a milieu for the participants to engage, to negotiate, and co-construct meanings with SELF and Others from critical perspectives. The foreign language learning experience serves as a contact zone in which the SELF is deconstructed and reconstructed through a constant interplay and negotiation of meaning with the OTHER. The drama syllabus and approaches furthered this inter-space experience, deepened the impact of encountering the OTHER, and thus enabled the process of recognizing and re-strengthening of one’s own cultural identity. The evidence in the research demonstrated that, when given appropriate opportunities, the EFL learners are able to develop critical intercultural awareness though the language learning experiences. A model for the development of such intercultural education is then constructed through this study. The research thus argues for a need of a critical pedagogy approach in the foreign language classroom