Predicting mechanical properties of silk from its amino acid sequences via machine learning.

The silk fiber is increasingly being sought for its superior mechanical properties, biocompatibility, and eco-friendliness, making it promising as a base material for various applications. One of the characteristics of protein fibers, such as silk, is that their mechanical properties are significantly dependent on the amino acid sequence. Numerous studies have been conducted to determine the specific relationship between the amino acid sequence of silk and its mechanical properties. Still, the relationship between the amino acid sequence of silk and its mechanical properties is yet to be clarified. Other fields have adopted machine learning (ML) to establish a relationship between the inputs, such as the ratio of different input material compositions and the resulting mechanical properties. We have proposed a method to convert the amino acid sequence into numerical values for input and succeeded in predicting the mechanical properties of silk from its amino acid sequences. Our study sheds light on predicting mechanical properties of silk fiber from respective amino acid sequences.

Relating spidroin motif prevalence and periodicity to the mechanical properties of major ampullate spider silks.

Spider dragline fibers exhibit incredible mechanical properties, outperforming many synthetic polymers in toughness assays, and possess desirable properties for medical and other human applications. These qualities make dragline fibers popular subjects for biomimetics research. The enormous diversity of spiders presents both an opportunity for the development of new bioinspired materials and a challenge for the identification of fundamental design principles, as the mechanical properties of dragline fibers show both intraspecific and interspecific variations. In this regard, the stress-strain curves of draglines from different species have been shown to be effectively compared by the α* parameter, a value derived from maximum-supercontracted silk fibers. To identify potential molecular mechanisms impacting α* values, here we analyze spider fibroin (spidroin) sequences of the Western black widow (Latrodectus hesperus) and the black and yellow garden spider (Argiope aurantia). This study serves as a primer for investigating the molecular properties of spidroins that underlie species-specific α* values. Initial findings are that while overall motif composition was similar between species, certain motifs and higher level periodicities of glycine-rich region lengths showed variation, notably greater distances between poly-A motifs in A. aurantia sequences. In addition to increased period lengths, A. aurantia spidroins tended to have an increased prevalence of charged and hydrophobic residues. These increases may impact the number and strength of hydrogen bond networks within fibers, which have been implicated in conformational changes and formation of nanocrystals, contributing to the greater extensibility of A. aurantia draglines compared to those of L. hesperus.

In situ three-dimensional spider web construction and mechanics.

Spiders are nature's engineers that build lightweight and high-performance web architectures often several times their size and with very few supports; however, little is known about web mechanics and geometries throughout construction, especially for three-dimensional (3D) spider webs. In this work, we investigate the structure and mechanics for a Tidarren sisyphoides spider web at varying stages of construction. This is accomplished by imaging, modeling, and simulations throughout the web-building process to capture changes in the natural web geometry and the mechanical properties. We show that the foundation of the web geometry, strength, and functionality is created during the first 2 d of construction, after which the spider reinforces the existing network with limited expansion of the structure within the frame. A better understanding of the biological and mechanical performance of the 3D spider web under construction could inspire sustainable robust and resilient fiber networks, complex materials, structures, scaffolding, and self-assembly strategies for hierarchical structures and inspire additive manufacturing methods such as 3D printing as well as inspire artistic and architectural and engineering applications.

Morus alba: Host reaction for Meloidogyne javanica, biological nematicides assessment and study of these relationships with yield and quality of leaves, cocoon and health of the silkworm.

Root-knot nematodes cause damage to several crops and the importance of each species can vary according with the crop and the agricultural region. In Brazil, Meloidogyne javanica is one of the most important nematode species parasitizing mulberry. To define management strategies, it is important to know if the crop species is damaged by the parasitism of the nematode and the best choices for control, as the use of nematicides. Biological nematicides have been extensively used in Brazil, but no information regarding its efficiency to control M. javanica in mulberry is available. Besides, it is not known if biological nematicides could improve the quality of leaves or if they alter the nutrient composition of leaves, which could interfere in the development of the silkworms that are feed with these leaves or in the quality of the silk produced. With the aim to address these questions, we propose a study that will start in the phenotyping of the main Brazilian mulberry cultivars to Meloidogyne species, passing through the test of efficiency of biological nematicides in the control of M. javanica in mulberry cultivar Miura, evaluation of the amount and quality of leaves produced and, using these leaves to feed silkworms, in the analyzes of the impact of these diet in the health of silkworms, and in the production and quality of the silk.

Complex behavioral plasticity is not reduced in spiderlings with miniature brains.

The brains of smaller animals are smaller than those of their larger relatives, but it is not clear whether their adaptive behavioral flexibility is more limited. Previous interspecific comparisons found that aspects of web construction behavior of very small orb weaving spiders (0.005 mg) were no less precise than those of much larger related orb weavers (30 mg), but the behaviors tested were relatively simple. Here we perform a more sensitive intraspecific test involving the multiple behavioral adjustments of orb web designs made by Leucauge argyra to confinement in very small spaces. Web adjustments of spiderlings as small as ~0.1 mg were compared to previously published observations of ~80 mg conspecific adults. Spiderlings in constrained spaces made all of the complex adjustments made by adults in at least seven independent web design variables, and their adjustments were no less precise. Rough estimates based on previously published data on total brain volumes and the mean diameters of neuron cell bodies suggested that spiderlings and adult females of Leucauge may have similar numbers of neurons, due to spiderlings having smaller neurons and a greater percentage of body tissues dedicated to the brain. We speculate that this neural similarity may explain why L. argyra spiderlings showed no behavioral deficits compared with adults.

Interpreting nature's finest insect silks (Order Embioptera): hydropathy, interrupted repetitive motifs, and fiber-to-film transformation for two neotropical species.

Silks produced by webspinners (Order Embioptera) interact with water by transforming from fiber to film, which then becomes slippery and capable of shedding water. We chose to explore this mechanism by analyzing and comparing the silk protein transcripts of two species with overlapping distributions in Trinidad but from different taxonomic families. The transcript of one, Antipaluria urichi (Clothodidae), was partially characterized in 2009 providing a control for our methods to characterize a second species: Pararhagadochir trinitatis (Scelembiidae), a family that adds to the taxon sampling for this little known order of insects. Previous reports showed that embiopteran silk protein (dubbed Efibroin) consists of a protein core of repetitive motifs largely composed of glycine (Gly), serine (Ser), and alanine (Ala) and a highly conserved C-terminal region. Based on mRNA extracted from silk glands, Next Generation sequencing, and de novo assembly, P. trinitatis silk can be characterized by repetitive motifs of Gly-Ser followed periodically by Gly-Asparagine (Asn-an unusual amino acid for Efibroins) and by a lack of Ala which is otherwise common in Efibroins. The putative N-terminal domain, composed mostly of polar, charged and bulky amino acids, is ten amino acids long with cysteine in the 10th position-a feature likely related to stabilization of the silk fibers. The 29 amino acids of the C-terminus for P. trinitatis silk closely resemble that of other Efibroin sequences, which show 74% shared identity on average. Examination of hydropathicity of Efibroins of both P. trinitatis and An. urichi revealed that these proteins are largely hydrophilic despite having a thin lipid coating on each nano-fiber. We deduced that the hydrophilic quality differs for the two species: due to Ser and Asn for P. trinitatis silk and to previously undetected spacers in An. urichi silk. Spacers are known from some spider and silkworm silks but this is the first report of such for Embioptera. Analysis of hydropathicity revealed the largely hydrophilic quality of these silks and this feature likely explains why water causes the transformation from fiber to film. We compared spun silk to the transcript and detected not insignificant differences between the two measurements implying that as yet undetermined post-translational modifications of their silk may occur. In addition, we found evidence for codon bias in the nucleotides of the putative silk transcript for P. trinitatis, a feature also known for other embiopteran silk genes.

Slingshot spiders build tensed, underdamped webs for ultrafast launches and speedy halts.

We develop a mathematical model to capture the web dynamics of slingshot spiders (Araneae: Theridiosomatidae), which utilize a tension line to deform their orb webs into conical springs to hunt flying insects. Slingshot spiders are characterized by their ultrafast launch speeds and accelerations (exceeding 1300 [Formula: see text]), however a theoretical approach to characterize the underlying spatiotemporal web dynamics remains missing. To address this knowledge gap, we develop a 2D-coupled damped oscillator model of the web. Our model reveals three key insights into the dynamics of slingshot motion. First, the tension line plays a dual role: enabling the spider to load elastic energy into the web for a quick launch (in milliseconds) to displacements of 10-15 body lengths, but also enabling the spider to halt quickly, attenuating inertial oscillations. Second, the dominant energy dissipation mechanism is viscous drag by the silk lines - acting as a low Reynolds number parachute. Third, the web exhibits underdamped oscillatory dynamics through a finely-tuned balance between the radial line forces, the tension line force and viscous drag dissipation. Together, our work suggests that the conical geometry and tension-line enables the slingshot web to act as both an elastic spring and a shock absorber, for the multi-functional roles of risky predation and self-preservation.

Aerodynamics and the role of the earth's electric field in the spiders' ballooning flight.

Some spiders aerially disperse relying on their fine fibres. This behaviour has been known as 'ballooning'. Observations on the ballooning behaviour of spiders have a long history and have more recently received special attention, yet its underlying physics is still poorly understood. It was traditionally believed that spiders rely on the airflows by atmospheric thermal convection to do ballooning. However, a recent experiment showed that exposure to an electric field alone can induce spiders' pre-ballooning behaviours (tiptoe and dropping/dangling) and even pulls them upwards in the air. The controversy between explanations of ballooning by aerodynamic flow or the earth's electric field has long existed. The major obstacle in studying the physics of ballooning is the fact that airflow and electric field are both invisible and our naked eyes can hardly recognise the ballooning silk fibres of spiders. This review explores the theory and evidence for the physical mechanisms of spiders' ballooning connects them to the behavioural physiology of spiders for ballooning. Knowledge gaps that need to be addressed in future studies are identified.

Evolutionary kinematics of spinneret movements for rapid silk thread anchorage in spiders.

Many organisms secrete structural materials from their bodies to enhance protection, foraging or signalling. The function of such secretion products can be further extended by their assembly into complex structures, so-called extended phenotypes, such as shells, nests and biofilms. Understanding the variation in the efficacy of such assembly processes could help to explain why extended phenotypes are common on some lineages and rare in others. Here, I comparatively studied the assembly of sticky silk fibres into thread anchorages by the innate 'printing' behaviour in 92 species of spiders from 45 families, representing the so-far largest comparative study of construction-related motion patterns. I found a global evolutionary trend towards a faster production of silk thread anchorages, in both web builders and hunting spiders. The slowest producers of silk anchors belong to a clade with an ancestral configuration of respiratory organs, suggesting that a major constraint to the evolution of spinning speed is the efficiency of oxygen uptake. Motion patterns were found to contain a high phylogenetic signal, but did not correlate with spinning speeds. These results help to explain the variation in diversity and ecological success among the spider fauna and showcase the value of comparative kinematics in biodiversity studies.

Ultrafast launch of slingshot spiders using conical silk webs.

In the Theridiosomatidae spider family, at least three genera (Epeirotypus, Naatlo and Theridiosoma) use their three-dimensional cone-shaped webs as ultrafast slingshots that catapult both the spider and the web towards prey [1-3]. Also known as slingshot spiders, theridiosomatids build three-dimensional conical webs with a tension line directly attached to the center of the web. In 1932, Hingston [1] hypothesized that the slingshot spider releases the tension line using its front legs, while holding the web with its rear legs. Coddington [2] detailed how female spiders meticulously build their webs line-by-line. But lacking to date has been quantification of spider kinematics, such as displacement, velocity and acceleration. Here we report the first quantification of theridiosomatid motion, revealing that slingshot spiders generate the fastest arachnid full body motion through use of their webs for external latch-mediated spring actuation [4].

Glandular innovations for a tunnelling life: Silk and associated leg glands in Melissotarsus and Rhopalomastix queen and worker ants.

As in other Hymenoptera, adult ants cannot secrete silk, unlike the larvae that spin a cocoon prior to metamorphosis. Fisher and Robertson (1999) first showed the existence of a silk gland in the head of adult Melissotarsus beccarii workers, and we confirm this with detailed histology and ultrastructural comparisons of both queens and workers. This African genus exhibits extreme morphological adaptations (legs, head shape and mandibular muscles) for tunnelling behaviour inside living trees, that underlie an obligate mutualism with scale insects. Rhopalomastix is its sister genus distributed across Asia, and we show that queens and workers also have a silk gland. This lineage of minute workers relies on silk to secure their network of tunnels against other arboreal ants. We show striking differences between these genera in the anatomy and ultrastructure of the cells that secrete silk, especially numerous vacuoles and an unexpectedly branched end apparatus in Melissotarsus. Moreover, the legs of Melissotarsus are much more specialized for tunnelling, and this includes highly expanded basitarsi. The latter house the novel 'Delage-Darchen gland', and we document its anatomy and ultrastructure, suggesting a proteinaceous secretion to harden roofs made of silk combined with wood fragments. The restriction of the Delage-Darchen gland to Melissotarsus, combined with a modified silk gland (an almost three-fold increase in the number of secretory cells, and ultrastructural differences suggestive of higher secretory activity), are evidence of an outstanding evolutionary divergence relative to Rhopalomastix. Synthesis of silk by adults is a significant innovation among ants, but its augmented production in Melissotarsus makes them better adapted for the hazards of arboreal life.

Mechanical Properties and Weibull Scaling Laws of Unknown Spider Silks.

Spider silks present extraordinary mechanical properties, which have attracted the attention of material scientists in recent decades. In particular, the strength and the toughness of these protein-based materials outperform the ones of many man-made fibers. Unfortunately, despite the huge interest, there is an absence of statistical investigation on the mechanical properties of spider silks and their related size effects due to the length of the fibers. Moreover, several spider silks have never been mechanically tested. Accordingly, in this work, we measured the mechanical properties and computed the Weibull parameters for different spider silks, some of them unknown in the literature. We also measured the mechanical properties at different strain rates for the dragline of the species Cupiennius salei. For the same species, we measured the strength and Weibull parameters at different fiber lengths. In this way, we obtained the spider silk scaling laws directly and according to Weibull's prediction. Both length and strain rates affect the mechanical properties of spider silk, as rationalized by Weibull's statistics.

The benthic sea-silk-thread displacement of a sessile bivalve, Pinctada imbricata radiata (Leach, 1819) in the Arabian-Persian Gulf.

A number of molluscs within the Class Bivalvia are defined by their ability to secrete fine silk like threads known as byssus which are used to anchor themselves to solid substrates. With relatively few exceptions the majority of these species remain in a sedentary state throughout their life attached via their byssal threads. However, observations of adult Pinctada imbricata radiata pearl oysters made during this study revealed this species' ability to implement active movement. Byssal threads were secreted in a sequence of attachment and detachment phases, which resulted in the active displacement of the oyster. The oyster was observed, in the laboratory over a 9 day period, travelling a distance of 28cm in a horizontal path. After horizontal displacement, a vertical climbing phase was observed until the oyster reached the water surface at which point the byssus was discarded and the animal dropped, drifting in accordance with water current intensity. It is possible that these adaptations of byssal use are a result of environmentally induced evolutionary change within P. i. radiata.

A study of the extraordinarily strong and tough silk produced by bagworms.

Global ecological damage has heightened the demand for silk as 'a structural material made from sustainable resources'. Scientists have earnestly searched for stronger and tougher silks. Bagworm silk might be a promising candidate considering its superior capacity to dangle a heavy weight, summed up by the weights of the larva and its house. However, detailed mechanical and structural studies on bagworm silks have been lacking. Herein, we show the superior potential of the silk produced by Japan's largest bagworm, Eumeta variegata. This bagworm silk is extraordinarily strong and tough, and its tensile deformation behaviour is quite elastic. The outstanding mechanical property is the result of a highly ordered hierarchical structure, which remains unchanged until fracture. Our findings demonstrate how the hierarchical structure of silk proteins plays an important role in the mechanical property of silk fibres.

Did aculeate silk evolve as an antifouling material?

Many of the challenges we currently face as an advanced society have been solved in unique ways by biological systems. One such challenge is developing strategies to avoid microbial infection. Social aculeates (wasps, bees and ants) mitigate the risk of infection to their colonies using a wide range of adaptations and mechanisms. These adaptations and mechanisms are reliant on intricate social structures and are energetically costly for the colony. It seems likely that these species must have had alternative and simpler mechanisms in place to ensure the maintenance of hygienic domicile conditions prior to the evolution of these complex behaviours. Features of the aculeate coiled-coil silk proteins are reminiscent of those of naturally occurring α-helical antimicrobial peptides (AMPs). In this study, we demonstrate that peptides derived from the aculeate silk proteins have antimicrobial activity. We reconstruct the predicted ancestral silk sequences of an aculeate ancestor that pre-dates the evolution of sociality and demonstrate that these ancestral sequences also contained peptides with antimicrobial properties. It is possible that the silks evolved as an antifouling material and facilitated the evolution of sociality. These materials serve as model materials for consideration in future biomaterial development.

An observational study of ballooning in large spiders: Nanoscale multifibers enable large spiders' soaring flight.

The physical mechanism of aerial dispersal of spiders, "ballooning behavior," is still unclear because of the lack of serious scientific observations and experiments. Therefore, as a first step in clarifying the phenomenon, we studied the ballooning behavior of relatively large spiders (heavier than 5 mg) in nature. Additional wind tunnel tests to identify ballooning silks were implemented in the laboratory. From our observation, it seems obvious that spiders actively evaluate the condition of the wind with their front leg (leg I) and wait for the preferable wind condition for their ballooning takeoff. In the wind tunnel tests, as-yet-unknown physical properties of ballooning fibers (length, thickness, and number of fibers) were identified. Large spiders, 16-20 mg Xysticus spp., spun 50-60 nanoscale fibers, with a diameter of 121-323 nm. The length of these threads was 3.22 ± 1.31 m (N = 22). These physical properties of ballooning fibers can explain the ballooning of large spiders with relatively light updrafts, 0.1-0.5 m s-1, which exist in a light breeze of 1.5-3.3 m s-1. Additionally, in line with previous research on turbulence in atmospheric boundary layers and from our wind measurements, it is hypothesized that spiders use the ascending air current for their aerial dispersal, the "ejection" regime, which is induced by hairpin vortices in the atmospheric boundary layer turbulence. This regime is highly correlated with lower wind speeds. This coincides well with the fact that spiders usually balloon when the wind speed is lower than 3 m s-1.

Silk fibroin preserves beta cell function under inflammatory stress while stimulating islet cell surface GLUT2 expression.

Silk fibroin is a novel biomaterial for enhancing transplanted islet cell function and survival. This study investigated whether silk fibroin may have unique properties that improve islet function in the face of inflammatory-mediated stress during transplantation. Murine islet function was tested in vitro with either silk fibroin or alginate and challenged with inflammatory cytokines. The glucose-stimulated insulin secretion index for all conditions decreased with inflammatory cytokines, but was better preserved for islets exposed to silk compared to those exposed to alginate or medium. GLUT2 transporter expression on the cell surface of islets exposed to silk was increased compared to alginate or medium alone. Upon cytokine stress, a greater percentage of islet cells exposed to silk expressed GLUT2 on their surface. We conclude that preconditioning islets with silk fibroin stimulates islet cell surface GLUT2 expression, an increase, which persists under inflammatory stress, and may improve islet engraftment and function after transplantation.

Intrinsic antimicrobial properties of silk spun by genetically modified silkworm strains.

The domesticated silkworm, Bombyx mori, is a fundamental insect for silk industry. Silk is obtained from cocoons, protective envelopes produced during pupation and composed of single raw silk filaments secreted by the insect silk glands. Currently, silk is used as a textile fibre and to produce new materials for technical and biomedical applications. To enhance the use of both fabrics and silk-based materials, great efforts to obtain silk with antimicrobial properties have been made. In particular, a convincing approach is represented by the enrichment of the textile fibre with antimicrobial peptides, the main effectors of the innate immunity. To this aim, silkworm-based transgenic techniques appear to be cost-effective strategies to obtain cocoons in which antimicrobial peptides are integrated among the silk proteins. Recently, cocoons transgenic for a recombinant silk protein conjugated to the silkworm Cecropin B antimicrobial peptide were obtained and showed enhanced antibacterial properties (Li et al. in Mol Biol Rep 42:19-25, https://doi.org/10.1007/s11033-014-3735-z , 2015a). In this work we used the piggyBac-mediated germline transformation to generate several transgenic B. mori lines able to overexpress Cecropin B or Moricin antimicrobial peptides at the level of the silk gland. The derived cocoons were characterised by increased antimicrobial properties and the resulting silk fibre was able to inhibit the bacterial growth of the Gram-negative Escherichia coli. Our results suggest that the generation of silkworm overexpressing unconjugated antimicrobial peptides in the silk gland might represent an additional strategy to obtain antimicrobial peptide-enriched silk, for the production of new silk-based materials.

Silk gene expression of theridiid spiders: implications for male-specific silk use.

Spiders (order Araneae) rely on their silks for essential tasks, such as dispersal, prey capture, and reproduction. Spider silks are largely composed of spidroins, members of a protein family that are synthesized in silk glands. As needed, silk stored in silk glands is extruded through spigots on the spinnerets. Nearly all studies of spider silks have been conducted on females; thus, little is known about male silk biology. To shed light on silk use by males, we compared silk gene expression profiles of mature males to those of females from three cob-web weaving species (Theridiidae). We de novo assembled species-specific male transcriptomes from Latrodectus hesperus, Latrodectus geometricus, and Steatoda grossa followed by differential gene expression analyses. Consistent with their complement of silk spigots, male theridiid spiders express appreciable amounts of aciniform, major ampullate, minor ampullate, and pyriform spidroin genes but not tubuliform spidroin genes. The relative expression levels of particular spidroin genes varied between sexes and species. Because mature males desert their prey-capture webs and become cursorial in their search for mates, we anticipated that major ampullate (dragline) spidroin genes would be the silk genes most highly expressed by males. Indeed, major ampullate spidroin genes had the highest expression in S. grossa males. However, minor ampullate spidroin genes were the most highly expressed spidroin genes in L. geometricus and L. hesperus males. Our expression profiling results suggest species-specific adaptive divergence of silk use by male theridiids.

A bioinspired adaptive spider web.

This work presents an adaptive structure inspired by spider webs' behavior. To investigate the dynamic properties and performance of this system, numerical models are developed to examine the effects of pretension in radial strings, and Young's modulus, and damping ratio on the natural frequency and total energy of the system. An experimental study was conducted to validate theoretical results. Stepper motors controlled by a microcontroller are utilized to increase the pretension in the radial strings of the web in order to tune the web's energy absorption ability. It is demonstrated that the pretension, Young's modulus, and damping ratio in the radial strings can significantly affect the natural frequency and total energy of full and damaged webs. It is also shown that increasing the pretension in the radial strings compensates for the loss of stiffness due to the damaged strings. Finally, it is shown that controlling the pretension in radial strings can provide higher energy absorption capability for the spider web.