Leveraging the model-experiment loop: Examples from cellular slime mold chemotaxis.

Interplay between models and experimental data advances discovery and understanding in biology, particularly when models generate predictions that allow well-designed experiments to distinguish between alternative mechanisms. To illustrate how this feedback between models and experiments can lead to key insights into biological mechanisms, we explore three examples from cellular slime mold chemotaxis. These examples include studies that identified chemotaxis as the primary mechanism behind slime mold aggregation, discovered that cells likely measure chemoattractant gradients by sensing concentration differences across cell length, and tested the role of cell-associated chemoattractant degradation in shaping chemotactic fields. Although each study used a different model class appropriate to their hypotheses - qualitative, mathematical, or simulation-based - these examples all highlight the utility of modeling to formalize assumptions and generate testable predictions. A central element of this framework is the iterative use of models and experiments, specifically: matching experimental designs to the models, revising models based on mismatches with experimental data, and validating critical model assumptions and predictions with experiments. We advocate for continued use of this interplay between models and experiments to advance biological discovery.

Self-cleaving peptides for expression of multiple genes in Dictyostelium discoideum.

The social amoeba Dictyostelium discoideum is a model for a wide range of biological processes including chemotaxis, cell-cell communication, phagocytosis, and development. Interrogating these processes with modern genetic tools often requires the expression of multiple transgenes. While it is possible to transfect multiple transcriptional units, the use of separate promoters and terminators for each gene leads to large plasmid sizes and possible interference between units. In many eukaryotic systems this challenge has been addressed through polycistronic expression mediated by 2A viral peptides, permitting efficient, co-regulated gene expression. Here, we screen the most commonly used 2A peptides, porcine teschovirus-1 2A (P2A), Thosea asigna virus 2A (T2A), equine rhinitis A virus 2A (E2A), and foot-and-mouth disease virus 2A (F2A), for activity in D. discoideum and find that all the screened 2A sequences are effective. However, combining the coding sequences of two proteins into a single transcript leads to notable strain-dependent decreases in expression level, suggesting additional factors regulate gene expression in D. discoideum that merit further investigation. Our results show that P2A is the optimal sequence for polycistronic expression in D. discoideum, opening up new possibilities for genetic engineering in this model system.

Engineering complex communities by directed evolution.

Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.

Potential use of only Yb2O3 in producing dense Si3N4 ceramics with high thermal conductivity by gas pressure sintering.

Yb2O3 is an efficient sintering additive for enhancing not only thermal conductivity but also the high-temperature mechanical properties of Si3N4 ceramics. Here we report the fabrication of dense Si3N4 ceramics with high thermal conductivity by the gas pressure sintering of α-Si3N4 powder compacts, using only Yb2O3 as an additive, at 1900 °C under a nitrogen pressure of 1 MPa. The effects of Yb2O3 content, sample packing condition and sintering time on the densification, microstructure and thermal conductivity were investigated. Curves of the density plotted against the Yb2O3 content exhibited a characteristic 'N' shape with a local minimum at 3 mol% Yb2O3 and nearly complete densification below and above this concentration. The effects of the sample packing condition on the densification, microstructure and thermal conductivity strongly depended on the Yb2O3 content. The embedded condition led to more complete densification but also to a decrease in thermal conductivity from 119 to 94 W m-1 K-1 upon 1 mol% Yb2O3 addition. The sample packing condition had little effect on the density and thermal conductivity (102-106 W m-1 K-1) at 7 mol% Yb2O3. The thermal conductivity value was strongly related to the microstructure.

Effect of starting powders on the sintering of nanostructured ZrO2 ceramics by colloidal processing.

The effect of starting powders on the sintering of nanostructured tetragonal zirconia was evaluated. Suspensions were prepared with a concentration of 10 vol.% by mixing a bicomponent mixture of commercial powders (97 mol.% monoclinic zirconia with 3 mol.% yttria) and by dispersing commercially available tetragonal zirconia (3YTZ, Tosoh). The preparation of the slurry by bead-milling was optimized. Colloidal processing using 50 µm zirconia beads at 4000 rpm generated a fully deagglomerated suspension leading to the formation of high-density consolidated compacts (62% of the theoretical density (TD) for the bicomponent suspension). Optimum colloidal processing of the bicomponent suspension followed by the sintering of yttria and zirconia allowed us to obtain nanostructured tetragonal zirconia. Three different sintering techniques were investigated: normal sintering, two-step sintering and spark plasma sintering. The inhibition of grain growth in the bicomponent mixed powders in comparison with 3YTZ was demonstrated. The inhibition of the grain growth may have been caused by inter-diffusion of cations during the sintering.

Textured silicon nitride: processing and anisotropic properties.

Textured silicon nitride (Si3N4) has been intensively studied over the past 15 years because of its use for achieving its superthermal and mechanical properties. In this review we present the fundamental aspects of the processing and anisotropic properties of textured Si3N4, with emphasis on the anisotropic and abnormal grain growth of ß-Si3N4, texture structure and texture analysis, processing methods and anisotropic properties. On the basis of the texturing mechanisms, the processing methods described in this article have been classified into two types: hot-working (HW) and templated grain growth (TGG). The HW method includes the hot-pressing, hot-forging and sinter-forging techniques, and the TGG method includes the cold-pressing, extrusion, tape-casting and strong magnetic field alignment techniques for ß-Si3N4 seed crystals. Each processing technique is thoroughly discussed in terms of theoretical models and experimental data, including the texturing mechanisms and the factors affecting texture development. Also, methods of synthesizing the rodlike ß-Si3N4 single crystals are presented. Various anisotropic properties of textured Si3N4 and their origins are thoroughly described and discussed, such as hardness, elastic modulus, bending strength, fracture toughness, fracture energy, creep behavior, tribological and wear behavior, erosion behavior, contact damage behavior and thermal conductivity. Models are analyzed to determine the thermal anisotropy by considering the intrinsic thermal anisotropy, degree of orientation and various microstructure factors. Textured porous Si3N4 with a unique microstructure composed of oriented elongated ß-Si3N4 and anisotropic pores is also described for the first time, with emphasis on its unique mechanical and thermal-mechanical properties. Moreover, as an important related material, textured α-Sialon is also reviewed, because the presence of elongated α-Sialon grains allows the production of textured α-Sialon using the same methods as those used for textured ß-Si3N4 and ß-Sialon.