Present Model Systems Research Articles

Reciprocity relations in a biologically inspired nanomagnonic system with dipolar coupling

Magnetosome chains in magnetotactic bacteria present ideal nanomagnonic model systems for studying collective resonance modes of dipolar-coupled single domain particles in relation to their spatial arrangement. Using microresonator-based ferromagnetic resonance (FMR) spectroscopy, electron microscopy, and micromagnetic modeling, we here provide insights into the complex magnonic activity within a single magnetosome chain. While the angular dependence of its FMR spectrum is dominated by twofold symmetry features due to the uniaxial anisotropy of linear chain segments, we also observed an unexpected behavior such as interrupted lines and flat bands due to the intricate geometrical details of this particular chain, such as a cross-like structural anomaly where a pair of particles is oriented perpendicular to the main axis of the chain and thus breaks the prevailing axial dipolar coupling symmetry. Such a cross junction formed by four particles exhibits interesting magnonic network properties. Notably, we observe reciprocity in the sense that the spectral response of one particle to an excitation of another one is identical to the response of the latter given an excitation of the former. Furthermore, we have identified that magnonic coupling between A and B can be facilitated via a dark state, as in magnonic stimulated Raman adiabatic passage, and that this dark-state coupling can be made non-reciprocal between A and B by breaking the symmetry of the spatial arrangement of the four particles.

What we need to know about the germ-free animal models.

The gut microbiota (GM), as a forgotten organ, refers to the microbial community that resides in the gastrointestinal tract and plays a critical role in a variety of physiological activities in different body organs. The GM affects its targets through neurological, metabolic, immune, and endocrine pathways. The GM is a dynamic system for which exogenous and endogenous factors have negative or positive effects on its density and composition. Since the mid-twentieth century, laboratory animals are known as the major tools for preclinical research; however, each model has its own limitations. So far, two main models have been used to explore the effects of the GM under normal and abnormal conditions: the isolated germ-free and antibiotic-treated models. Both methods have strengths and weaknesses. In many fields of host-microbe interactions, research on these animal models are known as appropriate experimental subjects that enable investigators to directly assess the role of the microbiota on all features of physiology. These animal models present biological model systems to either study outcomes of the absence of microbes, or to verify the effects of colonization with specific and known microbial species. This paper reviews these current approaches and gives advantages and disadvantages of both models.

Pronounced interplay between intrinsic phase-coexistence and octahedral tilt magnitude in hole-doped lanthanum cuprates

Definitive understanding of superconductivity and its interplay with structural symmetry in the hole-doped lanthanum cuprates remains elusive. The suppression of superconductivity around 1/8th doping maintains particular focus, often attributed to charge-density waves (CDWs) ordering in the low-temperature tetragonal (LTT) phase. Central to many investigations into this interplay is the thesis that La1.875Ba0.125CuO4 and particularly La1.675Eu0.2Sr0.125CuO4 present model systems of purely LTT structure at low temperature. However, combining single-crystal and high-resolution powder X-ray diffraction, we find these to exhibit significant, intrinsic coexistence of LTT and low-temperature orthorhombic domains, typically associated with superconductivity, even at 10 K. Our two-phase models reveal substantially greater tilting of CuO6 octahedra in the LTT phase, markedly buckling the CuO2 planes. This would couple significantly to band narrowing, potentially indicating a picture of electronically driven phase segregation, reminiscent of optimally doped manganites. These results call for reassessment of many experiments seeking to elucidate structural and electronic interplay at 1/8 doping.

Functional Heterogeneity in Superorganisms: Emerging Trends and Concepts

Abstract Social insects are biological benchmarks of self-organization and decentralized control. Their integrated yet accessible nature makes them ideal models for the investigation of complex social network interactions, and the mechanisms that shape emergent group capabilities. Increasingly, interindividual heterogeneity, and the functional role that it may play, is seen as an important facet of colonies’ social architecture. Insect superorganisms present powerful model systems for the elucidation of conserved trends in biology, through the strong and consistent analogies that they display with multicellular organisms. As such, research relating to the benefits and constraints of heterogeneity in behavior, morphology, phenotypic plasticity, and colony genotype provides insight into the underpinnings of emergent collective phenomena, with rich potential for future exploration. Here, we review recent advances and trends in the understanding of functional heterogeneity within social insects. We highlight the scope for fundamental advances in biological knowledge, and the opportunity for emerging concepts to be verified and expanded upon, with the aid of bioinspired engineering in swarm robotics, and computational task allocation.

Mg2+ Diffusion-Induced Structural and Property Evolution in Epitaxial Fe3O4 Thin Films.

Epitaxial Fe3O4 thin films grown on single crystal MgO(001) present well-defined model systems to study fundamental multivalent ion diffusion and associated phase transition processes in transition-metal-oxide-based cathodes. In this work, we show at an atomic scale the Mg2+ diffusion pathways, kinetics, and reaction products at the Fe3O4/MgO heterostructures under different oxygen partial pressures but with the same thermal annealing conditions. Combining microscopic, optical, and spectroscopic techniques, we demonstrate that an oxygen-rich environment promotes facile Mg2+ incorporation into the Fe2+ sites, leading to the formation of Mg1-xFe2+xO4 spinel structures, where the corresponding portion of the Fe2+ ions are oxidized to Fe3+. Conversely, annealing in vacuum results in the formation of a thin interfacial rocksalt layer (Mg1-yFeyO), which serves as a blocking layer leading to significantly reduced Mg2+ diffusion to the bulk Fe3O4. The observed changes in transport and optical properties as a result of Mg diffusion are interpreted in light of the electronic structures determined by X-ray photoelectron spectroscopy and X-ray absorption spectroscopy. Our results reveal the critical role of available anions in governing cation diffusion in the spinel structures and the need to prevent formation of unwanted reaction intermediates for the promotion of facile cation diffusion.

Bacterial EPS in Agarose Hydrogels Directs Mineral Organization in Calcite Precipitates: Species-Specific Biosignatures of Bacillus subtilis, Mycobacterium phley, Mycobacterium smagmatis, and Pseudomonas putida EPS

Hydrogels present model systems for biopolymer matrices in biological structural materials, as their fabric and physicochemical properties can be tailored to mimic characteristics of polymer matrices in biological hard tissues. However, hydrogels comprise synthetic compounds and lack attributes of native biopolymers, in contrast to extracellular polymeric substance (EPS) actively secreted by microbes for protection and enhancement of physiological activities. For testing the directing influence of native biopolymers on mineralization, we precipitated calcite/gel composite aggregates from agarose gels containing EPS of Bacillus subtilis, Mycobacterium phley, Mycobacterium smagmatis, or Pseudomonas putida, respectively. We characterized the aggregates with Fourier transform infrared spectroscopy, field-emission scanning electron microscopy imaging, and electron backscatter diffraction. Relative to reference aggregates devoid of EPS, aggregates containing EPS are reduced in size and show distinctive morphologies directed by the EPS of a specific bacterium. In P. putida and M. phley composites, occluded polymers are present as membranes, for M. smagmatis and B. subtilis occluded polymers are mainly developed as networks of fibrils. Precipitate crystal subunit formation in EPS-containing composites is extensive compared to the reference crystal; subunits vary in shape, size, and organization: for M. smagmatis and B. subtilis, subunit organization is radial to spherulitic; for P. putida, it is random; for M. phley, it is coaligned in all three dimensions (single-crystal-like). Bacterial EPS changes mineral microstructure/texture in a species-specific manner, a characteristic that, when developed further, might be used as an identification tool for bacterial calcification in present/past environments.

Versatile and Dynamic Symbioses Between Insects and Burkholderia Bacteria.

Symbiotic associations with microorganisms represent major sources of ecological and evolutionary innovations in insects. Multiple insect taxa engage in symbioses with bacteria of the genus Burkholderia, a diverse group that is widespread across different environments and whose members can be mutualistic or pathogenic to plants, fungi, and animals. Burkholderia symbionts provide nutritional benefits and resistance against insecticides to stinkbugs, defend Lagria beetle eggs against pathogenic fungi, and may be involved in nitrogen metabolism in ants. In contrast to many other insect symbioses, the known associations with Burkholderia are characterized by environmental symbiont acquisition or mixed-mode transmission, resulting in interesting ecological and evolutionary dynamics of symbiont strain composition. Insect-Burkholderia symbioses present valuable model systems from which to derive insights into general principles governing symbiotic interactions because they are often experimentally and genetically tractable and span a large fraction of the diversity of functions, localizations, and transmission routes represented in insect symbioses.

Infrared spectral-shift induced by hydrogen bonding cooperativity in cyclic and prismatic water clusters

A direct representation of the cooperative vibrating properties of hydrogen bonds (H-bonds) is presented for cyclic and prismatic water clusters. Through collaborating nuclear vibrations, which are inherent in H-bonding, these weak bonds constitute a simple form of cooperativity, which gives H-bonds an unexpectedly amplified effect. Hence, abnormal shifting activities of infrared vibration modes are observed. The nuclear vibrating patterns clearly reveal that H-bonds retain three effects: i) arousing collective nuclear vibrations, ii) intensifying donor symmetric stretching modes (Symst), and iii) inhibiting donor asymmetric stretching modes (Asyst). H-bonds in aqueous systems show diverse cooperative behavior that originates from the versatile assembly of water molecules. For the first time, we directly show that “coherent” H-bonds reinforce Symst and restrict Asyst extremely powerfully, in contrast to incoherent H-bonds. However, anharmonic nuclear vibrations partially destabilize the cooperative effects of H-bonds. Beyond the present model systems, our findings advance a new perspective on the intrinsic cooperativity of H-bonding, and should stimulate incentives for future spectroscopic and biological dynamic studies.

Gapped boundary phases of topological insulators via weak coupling

The standard boundary state of a topological insulator in 3 + 1 dimensions has gapless charged fermions. We present model systems that reproduce this standard gapless boundary state in one phase, but also have gapped phases with topological order. Our models are weakly coupled and all the dynamics is explicit. We rederive some known boundary states of topological insulators and construct new ones. Consistency with the standard spin/charge relation of condensed matter physics places a nontrivial constraint on models.

Functional Properties of Human Stem Cell-Derived Neurons in Health and Disease.

Stem cell-derived neurons from various source materials present unique model systems to examine the fundamental properties of central nervous system (CNS) development as well as the molecular underpinnings of disease phenotypes. In order to more accurately assess potential therapies for neurological disorders, multiple strategies have been employed in recent years to produce neuronal populations that accurately represent in vivo regional and transmitter phenotypes. These include new technologies such as direct conversion of somatic cell types into neurons and glia which may accelerate maturation and retain genetic hallmarks of aging. In addition, novel forms of genetic manipulations have brought human stem cells nearly on par with those of rodent with respect to gene targeting. For neurons of the CNS, the ultimate phenotypic characterization lies with their ability to recapitulate functional properties such as passive and active membrane characteristics, synaptic activity, and plasticity. These features critically depend on the coordinated expression and localization of hundreds of ion channels and receptors, as well as scaffolding and signaling molecules. In this review I will highlight the current state of knowledge regarding functional properties of human stem cell-derived neurons, with a primary focus on pluripotent stem cells. While significant advances have been made, critical hurdles must be overcome in order for this technology to support progression toward clinical applications.

What Is the Main Driver of Ageing in Long-Lived Winter Honeybees: Antioxidant Enzymes, Innate Immunity, or Vitellogenin?

To date five different theories compete in explaining the biological mechanisms of senescence or ageing in invertebrates. Physiological, genetical, and environmental mechanisms form the image of ageing in individuals and groups. Social insects, especially the honeybee Apis mellifera, present exceptional model systems to study developmentally related ageing. The extremely high phenotypic plasticity for life expectancy resulting from the female caste system provides a most useful system to study open questions with respect to ageing. Here, we used long-lived winter worker honeybees and measured transcriptional changes of 14 antioxidative enzyme, immunity, and ageing-related (insulin/insulin-like growth factor signaling pathway) genes at two time points during hibernation. Additionally, worker bees were challenged with a bacterial infection to test ageing- and infection-associated immunity changes. Gene expression levels for each group of target genes revealed that ageing had a much higher impact than the bacterial challenge, notably for immunity-related genes. Antimicrobial peptide and antioxidative enzyme genes were significantly upregulated in aged worker honeybees independent of bacterial infections. The known ageing markers vitellogenin and IlP-1 were opposed regulated with decreasing vitellogenin levels during ageing. The increased antioxidative enzyme and antimicrobial peptide gene expression may contribute to a retardation of senescence in long-lived hibernating worker honeybees.

Doped Mott Insulators in (111) Bilayers of Perovskite Transition-Metal Oxides with a Strong Spin-Orbit Coupling

The electronic properties of Mott insulators realized in (111) bilayers of perovskite transition-metal oxides are studied. The low-energy effective Hamiltonians for such Mott insulators are derived in the presence of a strong spin-orbit coupling. These models are characterized by the antiferromagnetic Heisenberg interaction and the anisotropic interaction whose form depends on the d orbital occupancy. From exact diagonalization analyses on finite clusters, the ground state phase diagrams are derived, including a Kitaev spin liquid phase in a narrow parameter regime for t(2g) systems. Slave-boson mean-field analyses indicate the possibility of novel superconducting states induced by carrier doping into the Mott-insulating parent systems, suggesting the present model systems as unique playgrounds for studying correlation-induced novel phenomena. Possible experimental realizations are also discussed.

Self-Assembled Porphyrins on Modified Zinc Oxide Nanorods: Development of Model Systems for Inorganic–Organic Semiconductor Interface Studies

Dense arrays of zinc oxide nanorods with high specific surface areas were grown by hydrothermal method and functionalized by self-assembled monolayer (SAM) of porphyrins. The growth process was optimized to obtain dense arrays of nanorods with diameter of 60–80 nm and length up to 1.5 μm. The increase in the effective surface area was monitored by comparing the absorbances of SAM deposited both on the flat and nanorod surfaces of ZnO. To alter further semiconductor-organic SAM interactions, a 2 or 5 nm thick layer of either Al2O3 or TiO2 was deposited on the ZnO nanorods. The present results show that both carboxylic acid and triethoxysilane anchors can be used to form porphyrin SAMs on the studied metal oxide substrates, and the electronic interactions between the metal oxide and porphyrin SAM are strongly modified by a thin layer of Al2O3 or TiO2. These hybrid semiconductor-organic SAM constructions present promising model systems for advanced spectroscopy studies of semiconductor-organic interfaces with high degree of control over electronic interactions and system morphology.

Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets

We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is not caused by resonance-assisted hydrogen bonding (RAHB). This follows from extensive computational analyses of guanine quartets (G(4)) and xanthine quartets (X(4)) based on dispersion-corrected density functional theory (DFT-D). Our investigations cover the situation of quartets in the gas phase, in aqueous solution as well as in telomere-like stacks. A new mechanism for cooperativity between hydrogen bonds in guanine quartets emerges from our quantitative Kohn-Sham molecular orbital (MO) and corresponding energy decomposition analyses (EDA). Our analyses reveal that the intriguing cooperativity originates from the charge separation that goes with donor-acceptor orbital interactions in the σ-electron system, and not from the strengthening caused by resonance in the π-electron system. The cooperativity mechanism proposed here is argued to apply, beyond the present model systems, also to other hydrogen bonds that show cooperativity effects.

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

Pancreatic ductal adenocarcinoma (PDA) is a lethal disease. Overall survival is typically 6 months from diagnosis. Numerous phase 3 trials of agents effective in other malignancies have failed to benefit unselected PDA populations, although patients do occasionally respond. Studies in other solid tumors have shown that heterogeneity in response is determined, in part, by molecular differences between tumors. Furthermore, treatment outcomes are improved by targeting drugs to tumor subtypes in which they are selectively effective, with breast and lung cancers providing recent examples. Identification of PDA molecular subtypes has been frustrated by a paucity of tumor specimens available for study. We have overcome this problem by combined analysis of transcriptional profiles of primary PDA samples from several studies, along with human and mouse PDA cell lines. We define three PDA subtypes: classical, quasimesenchymal and exocrine-like, and we present evidence for clinical outcome and therapeutic response differences between them. We further define gene signatures for these subtypes that may have utility in stratifying patients for treatment and present preclinical model systems that may be used to identify new subtype specific therapies.

Theoretical study on the hydrogen bond interaction of 1:1 supermolecular complexes of protonated adrenaline with formate anion and its derivatives

The hydrogen bond (H-bond) interaction of 1:1 supermolecular complexes of protonated adrenaline (PAd +) with formate anion and its derivatives (denoted as RCOO −, R H, CH 3, CH 2F, CH 2Cl, and CH 2Br) has been investigated by performing density functional theory calculations at the B3LYP/6-31G+(d) level. We obtained the most stable three conformations for each complex, which are denoted as PAd +–RCOO −(I), PAd +–RCOO −(II), PAd +–RCOO −(III), respectively, and calculated the interaction energy between PAd + and RCOO −. In all PAd +–RCOO − complexes, PAd +–CH 3COO − is found to be the most favorable energetically. There exists low-barrier hydrogen bond (LBHB) in PAd +–HCOO −(III), PAd +–CH 2FCOO −(III), PAd +–CH 2ClCOO −(III), and PAd +–CH 2Br −(III) complexes. The solvent effects on the geometry and energy of the complexes are also considered by using the polarizable continuum model (PCM) model in aqueous solvent. It is found that PAd +–R − complexes in solution are significantly less stable than those in the gas-phase. The theoretical results for the present model systems will be useful for experimental researchers working in this field.

3D Brownian Diffusion of Submicron-Sized Particle Clusters

We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Since they could be separated into fractions of well-defined configurations on a sufficient scale and because their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle doublets, triplets, and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different hydrodynamic models for calculating the diffusion coefficients for objects with complex shapes could be applied. Because hydrodynamic friction must be restricted to the cluster surface, the so-called shell model, in which the surface is represented as a shell of small friction elements, was most suitable to describe the dynamics. A quantitative comparison of the predictions from theoretical modeling with the results obtained by DDLS showed an excellent agreement between experiment and theory.

Restricted gene flow in the endangered pygmy bluetongue lizard (Tiliqua adelaidensis) in a fragmented agricultural landscape

Habitat fragmentation can have several adverse genetic impacts on populations. Assessing the extent of these threatening processes is essential in conservation management. In the present study, we investigated the genetic population structure of the endangered pygmy bluetongue lizard, Tiliqua adelaidensis, which is now restricted to a few small fragments of its previously more extensive grassland habitat. The aim of our study was to investigate genetic diversity and gene flow both among and within sample sites. The information will assist in making recommendations for habitat conservation and translocation programs. We collected DNA from 229 individuals from six isolated sample sites and genotyped them for 16 polymorphic microsatellite loci. Across all six sample sites, observed heterozygosity ranged from 0.75 to 0.82. There was no evidence of population bottlenecks and little evidence of inbreeding due to consanguineous mating. Genetic differentiation was low to moderate although significant for all pairs of sample sites (FST = 0.021–0.091). Results from Bayesian clustering analyses revealed distinct clusters in the overall sample and suggested restricted gene flow between sample sites separated by distances ranging from 1.7 to 71.6 km. By using spatial autocorrelation, we also found a significant genetic structure within sample sites at distances up to 30 m, suggesting restricted gene flow even in small patches of continuous habitat. It will be important to preserve this finely clustered population structure in captive breeding and translocation programs. Increasing opportunities for gene flow through habitat corridors or population augmentation may help maintain genetic diversity and prevent an increase in differentiation. Although endangered species do not always present model systems for studying fragmentation, our approach shows how important genetic information can be acquired to aid conservation in highly fragmented ecosystems.

Application of the independent molecule model to elucidate the dynamics of structure I methane hydrate: A second report

Two model systems of methane hydrate are constructed. One has a small cage surrounded by 12 large cages. The other has a large cage surrounded by four small cages and ten large cages. Three different H-bonding network patterns between waters are formed, and three random configurations of methane in each cage are chosen. A new method called the surface water fixed model is presented in which the energy minimum conformations for both model systems are preserved close to the X-ray crystallized structure. With normal mode analysis, we calculated frequencies of 2916.6 cm −1 for a small cage at a centre, 2915.9 cm −1 not at a centre, and 2911.7 cm −1 for a large cage at a centre, and 2911.3 cm −1 not at a centre. These frequencies are in moderate agreement with the corresponding Raman spectra, though not adequate. With our new method, however, it should be possible to improve agreement with the Raman spectra, if a model system vastly larger than the present model systems were constructed.

Nondeterministic polynomial time factoring in the tile assembly model

Formalized study of self-assembly has led to the definition of the tile assembly model, Previously I presented ways to compute arithmetic functions, such as addition and multiplication, in the tile assembly model: a highly distributed parallel model of computation that may be implemented using molecules or a large computer network such as the Internet. Here, I present tile assembly model systems that factor numbers nondeterministically using Θ ( 1 ) distinct components. The computation takes advantage of nondeterminism, but theoretically, each of the nondeterministic paths is executed in parallel, yielding the solution in time linear in the size of the input, with high probability. I describe mechanisms for finding the successful solutions among the many parallel executions and explore bounds on the probability of such a nondeterministic system succeeding and prove that the probability can be made arbitrarily close to 1.