Old Acetogens, New Light

Acetogens utilize the acetyl-CoA Wood-Ljungdahl pathway as a terminal electron-accepting, energy-conserving, CO2-fixing process. The decades of research to resolve the enzymology of this pathway (1) preceded studies demonstrating that acetogens not only harbor a novel CO2-fixing pathway, but are also ecologically important, and (2) overshadowed the novel microbiological discoveries of acetogens and acetogenesis. The first acetogen to be isolated, Clostridium aceticum, was reported by Klaas Tammo Wieringa in 1936, but was subsequently lost. The second acetogen to be isolated, Clostridium thermoaceticum, was isolated by Francis Ephraim Fontaine and co-workers in 1942. C. thermoaceticum became the most extensively studied acetogen and was used to resolve the enzymology of the acetyl-CoA pathway in the laboratories of Harland Goff Wood and Lars Gerhard Ljungdahl. Although acetogenesis initially intrigued few scientists, this novel process fostered several scientific milestones, including the first 14C-tracer studies in biology and the discovery that tungsten is a biologically active metal. The acetyl-CoA pathway is now recognized as a fundamental component of the global carbon cycle and essential to the metabolic potentials of many different prokaryotes. The acetyl-CoA pathway and variants thereof appear to be important to primary production in certain habitats and may have been the first autotrophic process on earth and important to the evolution of life. The purpose of this article is to (1) pay tribute to those who discovered acetogens and acetogenesis, and to those who resolved the acetyl-CoA pathway, and (2) highlight the ecology and physiology of acetogens within the framework of their scientific roots

Old Acetogens, New Light

Acetogens utilize the acetyl-CoA Wood-Ljungdahl pathway as a terminal electron-accepting, energy-conserving, CO2-fixing process. The decades of research to resolve the enzymology of this pathway (1) preceded studies demonstrating that acetogens not only harbor a novel CO2-fixing pathway, but are also ecologically important, and (2) overshadowed the novel microbiological discoveries of acetogens and acetogenesis. The first acetogen to be isolated, Clostridium aceticum, was reported by Klaas Tammo Wieringa in 1936, but was subsequently lost. The second acetogen to be isolated, Clostridium thermoaceticum, was isolated by Francis Ephraim Fontaine and co-workers in 1942. C. thermoaceticum became the most extensively studied acetogen and was used to resolve the enzymology of the acetyl-CoA pathway in the laboratories of Harland Goff Wood and Lars Gerhard Ljungdahl. Although acetogenesis initially intrigued few scientists, this novel process fostered several scientific milestones, including the first 14C-tracer studies in biology and the discovery that tungsten is a biologically active metal. The acetyl-CoA pathway is now recognized as a fundamental component of the global carbon cycle and essential to the metabolic potentials of many different prokaryotes. The acetyl-CoA pathway and variants thereof appear to be important to primary production in certain habitats and may have been the first autotrophic process on earth and important to the evolution of life. The purpose of this article is to (1) pay tribute to those who discovered acetogens and acetogenesis, and to those who resolved the acetyl-CoA pathway, and (2) highlight the ecology and physiology of acetogens within the framework of their scientific roots

Ecological Drivers of Community Cohesion

From protocellular to societal, networks of living systems are complex and multiscale. Discerning the factors that facilitate assembly of these intricate interdependencies using pairwise interactions can be nearly impossible. To facilitate a greater understanding, we developed a mathematical and computational model based on a synthetic four-strain Saccharomyces cerevisiae interdependent system. Specifically, we aimed to provide a greater understanding of how ecological factors influence community dynamics. By leveraging transiently structured ecologies, we were able to drive community cohesion. We show how ecological interventions could reverse or slow the extinction rate of a cohesive community. An interconnected system first needs to persist long enough to be a subject of natural selection. Our emulation of Darwin’s “warm little ponds” with an ecology governed by transient compartmentalization provided the necessary persistence. Our results reveal utility across scales of organization, stressing the importance of cyclic processes in major evolutionary transitions, engineering of synthetic microbial consortia, and conservation biology.journal articl

Softening and Yielding of Soft Glassy Materials

Solids deform and fluids flow, but soft glassy materials, such as emulsions, foams, suspensions, and pastes, exhibit an intricate mix of solid and liquid-like behavior. While much progress has been made to understand their elastic (small strain) and flow (infinite strain) properties, such understanding is lacking for the softening and yielding phenomena that connect these asymptotic regimes. Here we present a comprehensive framework for softening and yielding of soft glassy materials, based on extensive numerical simulations of oscillatory rheological tests, and show that two distinct scenarios unfold depending on the material's packing density. For dense systems, there is a single, pressure-independent strain where the elastic modulus drops and the particle motion becomes diffusive. In contrast, for weakly jammed systems, a two-step process arises: at an intermediate softening strain, the elastic and loss moduli both drop down and then reach a new plateau value, whereas the particle motion becomes diffusive at the distinctly larger yield strain. We show that softening is associated with an extensive number of microscopic contact changes leading to a non-analytic rheological signature. Moreover, the scaling of the softening strain with pressure suggest the existence of a novel pressure scale above which softening and yielding coincide, and we verify the existence of this crossover scale numerically. Our findings thus evidence the existence of two distinct classes of soft glassy materials -- jamming dominated and dense -- and show how these can be distinguished by their rheological fingerprint.Comment: 9 pages, 11 figures, to appear in Soft Matte

Small and Medium Amplitude Oscillatory Shear Rheology of Model Branched Polystyrene (PS) Melts

Linear and nonlinear rheological properties of model comb polystyrenes (PS) with loosely to densely grafted architectures were measured under small and medium amplitude oscillatory shear (SAOS and MAOS) flow. This comb PS set had the same length of backbone and branches but varied in the number of branches from 3 to 120 branches. Linear viscoelastic properties of the comb PS were compared with the hierarchical model predictions. The model underpredicted zero-shear viscosity and backbone plateau modulus of densely branched comb with 60 or 120 branches because the model does not include the effect of side chain crowding. First- and third-harmonic nonlinearities reflected the hierarchy in the relaxation motion of comb structures. Notably, the low-frequency plateau values of first-harmonic MAOS moduli scaled with M$^{-2}$$_{w}$ (total molecular weight), reflecting dynamic tube dilution (DTD) by relaxed branches. Relative intrinsic nonlinearity Q$_{0}$ exhibited the difference between comb and bottlebrush via no low-frequency Q$_{0}$ peak of bottlebrush corresponding to backbone relaxation, which is probably related to the stretched backbone conformation in bottlebrush

Modulating the behavior of ethyl cellulose-based oleogels: The impact food-grade amphiphilic small molecules on structural, mechanical, and rheological properties

This work evaluates the ability of various lipid-based amphiphilic small molecules (ASMs) to modulate the mechanical and rheological properties of oleogels principally structured by ethyl cellulose (EC). Six ASMs varying in the chemical structure of their polar headgroups were used to produce EC-ASM oleogels. Stearic acid (StAc), monoacylglycerol (MAG), sodium stearoyl lactylate (SSL), and citric acid esters of monoglycerides (CITREM) all provided a dramatic enhancement in gel strength, while lactic acid (LACTEM) and acetic acid (ACETEM) esters produced only a marginal increase. Those additives which crystallized above 20 °C displayed pronounced changes in their network organization and crystal morphology in the presence of EC. Differences in the solid/liquid phase change behavior were also observed in select samples using differential scanning calorimetry. Both the small and large amplitude oscillatory shear responses were dependent on the ASM which was dependent on the chemistry of the headgroup, crystal network organization, and ability to plasticize the polymer network. The extent of thixotropic recovery was largely dependent on the polarity of functional groups in the ASMs, but was also influenced by the formation of a secondary crystal network. In general, ASMs which formed larger, system-spanning crystal networks (MAG, StAc) produced more brittle gels, while the highly hydrophilic, charged headgroup of SSL promoted a homogeneous distribution of small crystals, resulting in a tougher material. In the absence of a crystal network, stronger polar species in the ASM headgroup produced higher gel strength and increased elasticity. Thus, both ASM chemical structure and crystallization properties strongly contribute to the functionality of the resulting combined oleogelator systems

Yielding and Strain Stiffening in Entangled Assemblies of Frictional Granular Chains

Packings of macroscopic granular chains capture some of the essential aspects of molecular polymer systems and have been suggested as a paradigm to understand the physics on a molecular scale. However, here we demonstrate that the interparticle friction $\mu$ in granular chain packings, which has no counterpart in polymer systems, leads to a nontrivial yielding and rheological response. Based on discrete element simulations we study the nonlinear rheology of random packings of granular chains under large amplitude oscillatory shear. We find that the maximum stress and the penetration depth of the shear deformation into the material bulk are nonmonotonic functions of friction with extrema at intermediate values of $\mu$. We also show that the regularly repeated gaps between the adjacent grains, which are special to commercial granular chains, broaden the shear zone and enhance the entanglements in the system by promoting the interlocking events between chains. These topological constraints can significantly increase the degree of strain stiffening. Our findings highlight the differences between the physics of granular chain packings and molecular polymer systems.Comment: 7 pages, 5 figure