Aperiodic crystals in biology

Biological systems display a broad palette of hierarchically ordered designs spanning over many orders of magnitude in size. Remarkably enough, periodic order, which profusely shows up in nonliving ordered compounds, plays a quite subsidiary role in most biological structures, which can be appropriately described in terms of the more general aperiodic crystal notion instead. In this Topical Review I shall illustrate this issue by considering several representative examples, including botanical phyllotaxis, the geometry of cell patterns in tissues, the morphology of sea urchins, or the symmetry principles underlying virus architectures. In doing so, we will realize that albeit the currently adopted quasicrystal notion is not general enough to properly account for the rich structural features one usually finds in biological arrangements of matter, several mathematical tools and fundamental notions belonging to the aperiodic crystals science toolkit can provide a useful modeling framework to this end.

Automating cell counting in fluorescent microscopy through deep learning with c-ResUnet

Counting cells in fluorescent microscopy is a tedious, time-consuming task that researchers have to accomplish to assess the effects of different experimental conditions on biological structures of interest. Although such objects are generally easy to identify, the process of manually annotating cells is sometimes subject to fatigue errors and suffers from arbitrariness due to the operator’s interpretation of the borderline cases. We propose a Deep Learning approach that exploits a fully-convolutional network in a binary segmentation fashion to localize the objects of interest. Counts are then retrieved as the number of detected items. Specifically, we introduce a Unet-like architecture, cell ResUnet (c-ResUnet), and compare its performance against 3 similar architectures. In addition, we evaluate through ablation studies the impact of two design choices, (i) artifacts oversampling and (ii) weight maps that penalize the errors on cells boundaries increasingly with overcrowding. In summary, the c-ResUnet outperforms the competitors with respect to both detection and counting metrics (respectively, $$F_1$$ F 1 score = 0.81 and MAE = 3.09). Also, the introduction of weight maps contribute to enhance performances, especially in presence of clumping cells, artifacts and confounding biological structures. Posterior qualitative assessment by domain experts corroborates previous results, suggesting human-level performance inasmuch even erroneous predictions seem to fall within the limits of operator interpretation. Finally, we release the pre-trained model and the annotated dataset to foster research in this and related fields.

Organismal Design and Biomimetics: A Problem of Scale

Organisms and their features represent a complex system of solutions that can efficiently inspire the development of original and cutting-edge design applications: the related discipline is known as biomimetics. From the smallest to the largest, every species has developed and adapted different working principles based on their relative dimensional realm. In nature, size changes determine remarkable effects in organismal structures, functions, and evolutionary innovations. Similarly, size and scaling rules need to be considered in the biomimetic transfer of solutions to different dimensions, from nature to artefacts. The observation of principles that occur at very small scales, such as for nano- and microstructures, can often be seen and transferred to a macroscopic scale. However, this transfer is not always possible; numerous biological structures lose their functionality when applied to different scale dimensions. Hence, the evaluation of the effects and changes in scaling biological working principles to the final design dimension is crucial for the success of any biomimetic transfer process. This review intends to provide biologists and designers with an overview regarding scale-related principles in organismal design and their application to technical projects regarding mechanics, optics, electricity, and acoustics.

Bioinspired Helicoidal Composite Structure Featuring Functionally Graded Variable Ply Pitch

Composite laminated materials have been largely implemented in advanced applications due to the high tailorability of their mechanical performance and low weight. However, due to their low resistance against out-of-plane loading, they are prone to generate damage as a consequence of an impact event, leading to the loss of mechanical properties and eventually to the catastrophic failure of the entire structure. In order to overcome this issue, the high tailorability can be exploited to replicate complex biological structures that are naturally optimised to withstand extreme impact loading. Bioinspired helicoidal laminates have been already studied in-depth with good results; however, they have been manufactured by applying a constant pitch rotation between each consecutive ply. This is in contrast to that observed in biological structures where the pitch rotation is not constant along the thickness, but gradually increases from the outer shell to the inner core in order to optimise energy absorption and stress distribution. Based on this concept, Functionally Graded Pitch (FGP) laminated composites were designed and manufactured in order to improve the impact resistance relative to a benchmark laminate, exploiting the tough nature of helicoidal structures with variable rotation angles. To the authors’ knowledge, this is one of the first attempts to fully reproduce the helicoidal arrangement found in nature using a mathematically scaled form of the triangular sequence to define the lamination layup. Samples were subject to three-point bending and tested under Low Velocity Impact (LVI) conditions at 15 J and 25 J impact energies and ultrasonic testing was used to evaluate the damaged area. Flexural After Impact (FAI) tests were used to evaluate the post-impact residual energy to confirm the superior impact resistance offered by these bioinspired structures. Vast improvements in impact behaviour were observed in the FGP laminates over the benchmark, with an average reduction of 41% of the damaged area and an increase in post-impact residual energy of 111%. The absorbed energy was similarly reduced (−44%), and greater mechanical strength (+21%) and elastic energy capacity (+78%) were demonstrated in the three-point bending test.

Fabrication of 3D Micro-Blades for the Cutting of Biological Structures in a Microfluidic Guillotine

Micro-blade design is an important factor in the cutting of single cells and other biological structures. This paper describes the fabrication process of three-dimensional (3D) micro-blades for the cutting of single cells in a microfluidic “guillotine” intended for fundamental wound repair and regeneration studies. Our microfluidic guillotine consists of a fixed 3D micro-blade centered in a microchannel to bisect cells flowing through. We show that the Nanoscribe two-photon polymerization direct laser writing system is capable of fabricating complex 3D micro-blade geometries. However, structures made of the Nanoscribe IP-S resin have low adhesion to silicon, and they tend to peel off from the substrate after at most two times of replica molding in poly(dimethylsiloxane) (PDMS). Our work demonstrates that the use of a secondary mold replicates Nanoscribe-printed features faithfully for at least 10 iterations. Finally, we show that complex micro-blade features can generate different degrees of cell wounding and cell survival rates compared with simple blades possessing a vertical cutting edge fabricated with conventional 2.5D photolithography. Our work lays the foundation for future applications in single cell analyses, wound repair and regeneration studies, as well as investigations of the physics of cutting and the interaction between the micro-blade and biological structures.

Notes on Allometry and Prediction of Body Mass and Age of Giraffes

Quantification of how biological structures change during growth is essential for understanding how giraffes work. Allometry is the best arithmetical tool for analyzing changes that occur during growth. It measures how well the rate of change in one structure is associated with the rate of change in another in the species of interest. If the association is close, then allometry can be used, as in this chapter, to predict the age of a giraffe (from, say, its height) or its body mass (from its length and girth), with great accuracy. The best predictions are made if the data used to make predictions are derived from the particular species, and this type is referred to as ontogenetic allometry. A second type—interspecific allometry—uses data collected from other species to make predictions about the species of interest (like giraffes). Predictions using this second method are less accurate but are useful for establishing anatomical, physiological, and biochemical differences between the species of interest and all other comparable species.

Reparo de feridas na língua de camundongos jovens e velhos

Ageing affects several biological structures and mechanisms. The present work studied wound healing in 2 months old and 17 months old mice. Experimental wound in the tongue of 70 mice were performed. Histological diferences or similarities in healing ofyoung and aged mice were search. The results have shown that there were no ignificative differences on wound healing between young and aged groups. It was concluded that wound healing processes at the same rate independently of group age.