Learning from the biology of evolution: exaptation as a design strategy for future cities

PurposeThis paper highlights the importance of transdisciplinary studies in times of crisis. In the first part, the study shows the benefits of the introduction of literature on biology to better understand the evolutionary dynamics of architecture.Design/methodology/approachThe focus of the research concerns architectural exaptation. In biology, exaptation is a functional shift of a structure that already had a prior but different function. We will also learn that, in biology, all creative systems are redundant and involve variability and diversity.FindingsAs a conclusion, through the comparison between biology and architecture, we will, therefore, try to build an architectural taxonomy that demonstrates how indeterminism is not a subcategory of design. Instead, design paradigms in which redundancy and variable diversity of structures reflect functionalism constitute an equivalent and essential complement with respect to design determinism.Originality/valueIt demonstrates how architectural exaptation, intended as an indeterministic and radical mode of design, can contribute to overcoming the current global crisis because structural redundancy is frequently functional, mostly in ever-changing and unstable environments. For instance, the failure of a planned function of a city can be an opportunity to re-use a structure designed for an obsolete function to respond to unexpected constraints.

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model(HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements.

Functional Changes of T-Cell Subsets with Age and CMV Infection

Cytomegalovirus (CMV) latent infection and aging contribute to alterations in the function and phenotype of the T-cell pool. We have demonstrated that CMV-seropositivity is associated with the expansion of polyfunctional CD57+ T-cells in young and middle-aged individuals in response to different stimuli. Here, we expand our results on the effects of age and CMV infection on T-cell functionality in a cohort of healthy middle-aged and older individuals stratified by CMV serostatus. Specifically, we studied the polyfunctional responses (degranulation, IFN-γ and TNF-α production) of CD4+, CD8+, CD8+CD56+ (NKT-like), and CD4-CD8- (DN) T-cells according to CD57 expression in response to Staphylococcal Enterotoxin B (SEB). Our results show that CD57 expression by T-cells is not only a hallmark of CMV infection in young individuals but also at older ages. CD57+ T-cells are more polyfunctional than CD57− T-cells regardless of age. CMV-seronegative individuals have no or a very low percentages of cytotoxic CD4+ T-cells (CD1017a+) and CD4+CD57+ T-cells, supporting the notion that the expansion of these T-cells only occurs in the context of CMV infection. There was a functional shift in T-cells associated with CMV seropositivity, except in the NKT-like subset. Here, we show that the effect of CMV infection and age differ among T-cell subsets and that CMV is the major driving force for the expansion of highly polyfunctional CD57+ T-cells, emphasizing the necessity of considering CMV serology in any study of immunosenescence.

Modelling Functional Shifts in Two-Species Hypercycles

Research on hypercycles focuses on cooperative interactions among replicating species, including the emergence of catalytic parasites and catalytic shortcircuits. Further interactions may be expected to arise in cooperative systems. For instance, molecular replicators are subject to mutational processes and ecological species to behavioural shifts due to environmental and ecological changes. Such changes could involve switches from cooperative to antagonistic interactions, in what we call a functional shift. In this article, we investigate a model for a two-member hypercycle model, considering that one species performs a functional shift. First, we introduce the model dynamics without functional shifts to illustrate the dynamics only considering obligate and facultative cooperation. Then, two more cases maintaining cross-catalysis are considered: (i) a model describing the dynamics of ribozymes where a fraction of the population of one replicator degrades the other molecular species while the other fraction still receives catalytic aid; and (ii) a system in which a given fraction of the population predates on the cooperating species while the rest of the population still receives aid. We have characterised the key bifurcation parameters determining extinction, survival, and coexistence of species. We show that predation, regardless of the fraction that benefits from it, does not significantly change dynamics with respect to the degradative case (i), thus conserving dynamics and bifurcations. Their biological significance is interpreted, and their potential implications for the dynamics of early replicators and ecological species are outlined.

Analysis of pretreatment factors associated with stability in early class III treatment

Background The purpose of this study was to identify pretreatment factors associated with the stability of early class III treatment, since most orthodontists start the treatment with their uncertain hypotheses and/or predictions. Subjects consisted of 75 patients with a class III skeletal relationship (ANB < 2° and overjet < 0 mm) who had been consecutively treated with rapid maxillary expansion and facemask and followed until their second phase treatment. The patients were divided into two groups according to whether they showed relapse in follow-up. The stable group maintained their positive overjet (n = 55), and the unstable group experienced relapse with a zero or negative overjet (n = 20). Two general, three dental, and 13 cephalometric pretreatment factors were investigated to determine which factors were associated with stability. Results Sex, pretreatment age, and anteroposterior functional shift, which were hypothesized as associated factors, were not related to the stability of early class III treatment. Significant differences were detected between the two groups in the horizontal distance between the maxillary and mandibular molars in centric relation. Cephalometric variables, such as the mandibular length (Ar-Me), Wits appraisal, SN to ramus plane angle (SN-Rm), gonial angle, incisor mandibular plane angle (IMPA), and Frankfort plane to mandibular incisor angle (FMIA) showed significant differences between the groups. The horizontal distance was the most influential factor by logistic regression analysis. Conclusions Hypothesis (related to sex, age, functional shift) were rejected. Several cephalometric factors related to the mandible were associated with stability. The horizontal distance between the maxillary and mandibular molars in centric relation was the best predictor of early class III treatment relapse.

Simplified Fixed Technique for Correction of Anterior Crossbite: A Case Series

Anterior crossbites would normally require early intervention, especially when associated with mandibular displacements. The intervention would usually commence in children around the age of eight and nine, where treatment could be a challenge at this age. Therefore, a simple and quick treatment to this malocclusion would be desirable. This case series illustrates two cases of anterior crossbite with a functional shift that were successfully corrected using a simplified fixed technique, which involved a short-span nickel-titanium (Ni-Ti) aligning round archwire, composite resin and glass ionomer cement (GIC).

Reorganization of the Mitochondria-Organelle Interactome during Postnatal Development in Skeletal Muscle

Cellular development requires the integrated assembly of intracellular structures into functionally specialized regions supporting overall cellular performance. However, it remains unclear how coordination of organelle interactions contributes to development of functional specificity across cell types. Here, we utilize a subcellular connectomics approach to define the cell-scale reorganization of the mitochondria-organelle interactome across postnatal development in skeletal muscle. We show that while mitochondrial networks are disorganized and loosely associated with the contractile apparatus at birth, contact sites among mitochondria, lipid droplets, and the sarcoplasmic reticulum are highly abundant in neonatal muscles. The maturation process is characterized by a transition to highly organized mitochondrial networks wrapped tightly around the muscle sarcomere but also to less frequent interactions with both lipid droplets and the sarcoplasmic reticulum. These data demonstrate a developmental redesign reflecting a functional shift from muscle cell assembly supported by inter-organelle communication toward a muscle fiber highly specialized for contractile function.

Artificial Intelligence and Cheminformatics-guided Modern Privileged Scaffold Research

With the rapid development of computer science in scopes of theory, software, and hardware, artificial intelligence (mainly in the form of machine learning and more complex deep learning) combined with advanced cheminformatics is playing an increasingly important role in the drug discovery process. This development has also facilitated privileged scaffold-related research. By definition, a privileged scaffold is a structure that frequently occurs in diverse bioactive molecules. It either has a diverse family affinity or is selective to multiple family members in a superfamily, whilst is different from the “frequent hitters” or the “pan-assay interference compounds”. The long history of the use of this concept has witnessed a functional shift from stand-alone technology towards an integrated component in the drug discovery toolbox. Meanwhile, continuing efforts have been dedicated to deepen the understandings of the features of known privileged scaffolds. In this contribution, we focus on the current privileged scaffold-related research driven by state-of-art artificial intelligence approaches and cheminformatics. Representative cases with an emphasis on distinct research aspects are presented, including an update of the knowledge on privileged scaffolds; proof-of-concept tools and workflows to identify privileged scaffolds and to carry on de novo design; informatic SAR models with diversely complex data sets to provide an instructive prediction on new potential molecules bearing privileged scaffolds.

Comparative Evaluation of Microbiota Dynamics and Metabolites Correlation Between Spontaneous and Inoculated Fermentations of Nanfeng Tangerine Wine

Understanding the evolution of microorganisms and metabolites during wine fermentation is essential for controlling its production. The structural composition and functional capacity of the core microbiota determine the quality and quantity of fruit wine. Nanfeng tangerine wine fermentation involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this product fermentation remain unclear. Therefore, high-throughput sequencing (HTS) and headspace-gas chromatography-mass spectrometry (HS/GC-MS) were employed to reveal the core functional microbiota for the production of volatile flavors during spontaneous fermentation (SF) and inoculated fermentation (IF) with Saccharomyces cerevisiae of Nanfeng tangerine wine. A total of 13 bacterial and 8 fungal genera were identified as the core microbiota; Lactobacillus and Acetobacter were the dominant bacteria in SF and IF, respectively. The main fungal genera in SF and IF were Hanseniaspora, Pichia, and Saccharomyces with a clear succession. In addition, the potential correlations analysis between microbiota succession and volatile flavor dynamics revealed that Lactobacillus, Acetobacter, Hanseniaspora, and Saccharomyces were the major contributors to the production of the volatile flavor of Nanfeng tangerine wine. The results of the present study provide insight into the effects of the core functional microbiota in Nanfeng tangerine wine and can be used to develop effective strategies for improving the quality of fruit wines.