An artificial muscle actuator for biomimetic underwater propulsors

In this paper, we introduce the analytical framework of the modeling dynamic characteristics of a soft artificial muscle actuator for aquatic propulsor applications. The artificial muscle used for this underwater application is an ionic polymer-metal composite (IPMC) which can generate bending motion in aquatic environments. The inputs of the model are the voltages applied to multiple IPMCs, and the output can be either the shape of the actuators or the thrust force generated from the interaction between dynamic actuator motions and surrounding water. In order to determine the relationship between the input voltages and the bending moments, the simplified RC model is used, and the mechanical beam theory is used for the bending motion of IPMC actuators. Also, the hydrodynamic forces exerted on an actuator as it moves relative to the surrounding medium or water are added to the equations of motion to study the effect of actuator bending on the thrust force generation. The proposed method can be used for modeling the general bending type artificial muscle actuator in a single or segmented form operating in the water. The segmented design has more flexibility in controlling the shape of the actuator when compared with the single form, especially in generating undulatory waves. Considering an inherent nature of large deformations in the IPMC actuator, a large deflection beam model has been developed and integrated with the electrical RC model and hydrodynamic forces to develop the state space model of the actuator system. The model was validated against existing experimental data.     

A biomimetic platform for studying root-environment interaction

Aims

Microstructure plays an important role in biological systems. Microstructural features are critical in the interaction between two biological organisms, for example, a microorganism and the surface of a plant. However, isolating the structural effect of the interaction from all other parameters is challenging when working directly with the natural system. Replicating microstructure of leaves was recently shown to be a powerful research tool for studying leaf-environment interaction. However, no such tool exists for roots. Roots present a special challenge because of their delicacy (specifically of root hairs) and their 3D structure. We aim at developing such a tool for roots.

Methods

Biomimetics use synthetic systems to mimic the structure of biological systems, enabling the isolation of structural function. Here we present a method which adapts tools from leaf microstructure replication to roots. We introduce new polymers for this replication.

Results

We find that Polyurethane methacrylate (PUMA) with fast UV curing gives a reliable replication of the tomato root surface microstructure. We show that our system is compatible with the pathogenic soilborne bacterium Ralstonia solanacearum.

Conclusions

This newly developed tool may be used to study the effect of microstructure, isolated from all other effects, on the interaction of roots with their environment.

     

Micromachined biomimetic artificial haircell sensors

The biological haircell is a modular building block of a rich variety of biological sensors. Using micro- and nanofabrication technology, an engineering equivalent artificial haircell sensor can be developed, imitating the structure and transfer function of the biological haircell. The artificial haircells can be made of hybrid semiconductor, metal and polymers. This paper discusses a number of strategies, using representative material systems, for building artificial haircell sensors and briefly outlines their fabrication method and performance. The motivation for imitating the biological haircell is also discussed to provide a background for this work.     

An experimental assessment of artificial within-family selection for fitness in conservation programs

Equalizing familiar contributions is the simplest recommended strategy to maintain genetic diversity in conservation programs. However, this method implies a relaxation of natural selection and the possibility of accumulation of deleterious mutations. Computer simulations have shown that performing selection within families for fitness traits in a conservation program can be useful to alleviate such problems. We thus carried out an experiment with the model species Drosophila melanogaster in order to assess whether or not selection for fitness traits can be useful. We considered a fitness trait (pupa productivity) that was first checked to perform as a typical fitness component. The trait showed an inbreeding depression of 1.2 per 1 % increase in inbreeding and an asymmetrical response to selection with average realized heritabilities of about 0.04 in the upward direction and an order of magnitude larger (0.36) in the downward direction. The management experiment indicated that artificial within-family selection for fitness had only a marginal success for two reasons. First, there was not an appreciable decline in fitness across the experiment despite the low population sizes assumed (N = 10 or 20), even in the population not subjected to selection. This result is compatible with fitness models which imply the segregation of few deleterious mutations of large effect. Second, artificial selection within families had a limited impact on the trait, as one expects for a typical fitness component with very low heritability.     

植食性昆虫寄主植物嗅觉搜寻述介

植食性昆虫与寄主植物关系的本质是化学。植食性昆虫搜寻寄主的嗅觉媒介是植物气味即化学信息物质。在介绍植物气味构成及其扩散模型基础上,阐述了植物气味在地上植食性昆虫成虫、幼虫和地下植食性昆虫搜寻寄主过程中的嗅觉导向作用,并指出了今后相关研究需要注意的问题。从植物与环境因子的关系来看,植物气味包括构成性气味和诱发性气味两类,这两类气味的概念既相联系而又不同。构成性气味组分及构成因植物分类地位等而不同。诱发性气味组分因植食性昆虫取食、植物病原微生物、机械致伤等因子的胁迫而变化,这种变化性状随植物属和/或种、植株生长发育阶段、胁迫因子性质及其作用方式而不同。无论是哪种植物气味,其释放均具有节律性。气味扩散过程比较复杂,扩散状态可用数学模型表征。对于地上植食性昆虫成虫,植物气味对其寄主搜寻行为具有导向特异性,重点分析了这种特异性形成的两个假说;鳞翅目昆虫幼虫,能够利用植物化学信息物质趋向寄主植物或回避非寄主植物;地下植食性昆虫搜寻寄主,既与寄主植物地下组织释放或分泌的次级代谢物有关,又与一些初级代谢物有关。初级代谢物中的CO₂,起着“搜寻触发器”作用。有助于增强人们对昆虫与植...     

Doubly biomimetic catecholic phosphorylcholine copolymer: a platform strategy for fabricating antifouling surfaces

A doubly biomimetic PMNC polymer bearing cell antifouling phosphorylcholine and mussel adhesive protein catechol groups is synthesized. The polymer can be deposited onto a variety of substrates by dip-coating in an aqueous solution, adhering to surfaces via the catechol functional group while at the same time forming a cell outer membrane mimetic antifouling surface. Contact angle, ATR-FTIR and XPS measurements confirm polymer coating formation on a variety of inorganic and organic substrates. BSA and bovine plasma fibrinogen protein adsorption on PMNC coated surfaces are reduced significantly compared to unmodified substrates, and platelet adhesion from human serum onto the PMNC coated substrate surfaces is highly suppressed in this study.     

Synthesis and characterization of polyamine-based biomimetic catalysts as artificial ribonuclease

Several polyamine derivatives (I-V) conjugated with or without an intercalative moiety were prepared as ribonuclease mimics. Although no DNA-cleaving activity was observed for all compounds tested, mimics I, III, and V bearing an intercalative moiety along with the primary amine and/or imidazole moieties exhibited potent RNA-cleaving activity at near physiological pH. The RNA-cleaving reactions of the compounds show characteristic bell-shaped pH dependency, and the optimal pH values for III and V were well correlated to the pKa values of their active sites, primary amine, and imidazole moieties.     

An artificial receptor for glycoproteins

We describe the rational design, synthesis and development of a sterilizable biomimetic ligand for the affinity purification of glycoproteins. Based on mimicking the principles of natural carbohydrate recognition, a putative library of 196 glycoprotein-binding synthetic ligands was designed and synthesized on a polymeric support. Ligand 11/11, based on a triazine scaffold and immobilized on a hydrophilic support, was identified as the "lead" ligand. The carbohydrate recognizing the potential of the "lead" ligand was revealed by reduced binding of a periodate oxidized model glycoprotein, and by "sharp" elution profiles achieved with borate buffer eluents. Specific elution and competitive binding experiments determined the monosaccharide specificity of 11/11 in the order mannoside > glucoside > galactoside. The diastereo-selective performance of ligand 11/11 was quantified and reaffirmed by analytical affinity chromatography and (1)H-NMR, in the order galactoside < glucoside < mannoside with binding affinities (K(a), M(-1)) in the 63-214 and 20-83 M(-1) range, respectively. Partition coefficient analysis revealed binding constants towards glycoproteins in the 10(4) M(-1) range, that compared favourably with the affinities of carbohydrate binding lectins for glycoproteins, such as concanavalin A. Molecular modelling studies of ligand 11/11 revealed the formation of a pre-organized apolar "tweezer-like" cavity, containing complementary nitrogenous hydrogen bond donor and acceptor groups that formed selective interactions with the equatorial 3- and 4-hydroxyl groups of saccharides.     

Network mechanism for insect olfaction

Early olfactory pathway responses to the presentation of an odor exhibit remarkably similar dynamical behavior across phyla from insects to mammals, and frequently involve transitions among quiescence, collective network oscillations, and asynchronous firing. We hypothesize that the time scales of fast excitation and fast and slow inhibition present in these networks may be the essential element underlying this similar behavior, and design an idealized, conductance-based integrate-and-fire model to verify this hypothesis via numerical simulations. To better understand the mathematical structure underlying the common dynamical behavior across species, we derive a firing-rate model and use it to extract a slow passage through a saddle-node-on-an-invariant-circle bifurcation structure. We expect this bifurcation structure to provide new insights into the understanding of the dynamical behavior of neuronal assemblies and that a similar structure can be found in other sensory systems.     

PEPPeR, a platform for experimental proteomic pattern recognition

Quantitative proteomics holds considerable promise for elucidation of basic biology and for clinical biomarker discovery. However, it has been difficult to fulfill this promise due to over-reliance on identification-based quantitative methods and problems associated with chromatographic separation reproducibility. Here we describe new algorithms termed "Landmark Matching" and "Peak Matching" that greatly reduce these problems. Landmark Matching performs time base-independent propagation of peptide identities onto accurate mass LC-MS features in a way that leverages historical data derived from disparate data acquisition strategies. Peak Matching builds upon Landmark Matching by recognizing identical molecular species across multiple LC-MS experiments in an identity-independent fashion by clustering. We have bundled these algorithms together with other algorithms, data acquisition strategies, and experimental designs to create a Platform for Experimental Proteomic Pattern Recognition (PEPPeR). These developments enable use of established statistical tools previously limited to microarray analysis for treatment of proteomics data. We demonstrate that the proposed platform can be calibrated across 2.5 orders of magnitude and can perform robust quantification of ratios in both simple and complex mixtures with good precision and error characteristics across multiple sample preparations. We also demonstrate de novo marker discovery based on statistical significance of unidentified accurate mass components that changed between two mixtures. These markers were subsequently identified by accurate mass-driven MS/MS acquisition and demonstrated to be contaminant proteins associated with known proteins whose concentrations were designed to change between the two mixtures. These results have provided a real world validation of the platform for marker discovery.     

生物启发的细菌表面人造矿物壳:通过仿生矿化保护活细胞

【目的】生物启发的细菌表面仿生矿化人造矿物壳被用于保护活细胞。【方法】将细菌限制在坚固而完整的矿物壳中,有限的物理空间和物质交换使其暂时进行休眠,降低长期保存期间的活力损失以及提高在各种极端环境中的生存能力,并且能够通过酸去除矿物壳而重新激活细菌。【结果】相较于未仿生矿化的细菌(EcN),矿化细菌(EcN@CaCO₃)在32 d的储存实验中活力最高提升262倍;在pH 2.5的强酸环境中存活率提高837倍;在pH 12.0的强碱环境中存活率提高171倍;在80 ℃的高温条件下存活率提高59.1倍;甚至在抗生素溶液中,EcN@CaCO₃中细菌的存活率是EcN的729.7倍。【结论】本研究利用仿生矿化提高了细菌的保存稳定性,使其能在酸刺激下去除涂层恢复活性,也能在极端环境下保留细菌的活力,为微生物在环境生态、食品制造和生物医药等领域的应用提供研究基础。     

An efficient TILLING platform for cultivated tobacco

Targeting-induced local lesions in genomes(TILLING) is a powerful reverse-genetics tool that enables high-throughput screening of genomic variations in plants.Although TILLING has been developed for many diploid plants, the technology has been used in very few polyploid species due to their genomic complexity. Here, we established an efficient capillary electrophoresis-based TILLING platform for allotetraploid cultivated tobacco(Nicotiana tabacum L.) using an ethyl methanesulfonate(EMS)-mutagenized population of 1,536 individuals. We optimized the procedures for endonuclease preparation,leaf tissue sampling, DNA extraction, normalization,pooling, PCR amplification, heteroduplex formation, and capillary electrophoresis. In a test screen using seven target genes with eight PCR fragments, we obtained 118 mutants. The mutation density was estimated to be approximately one mutation per 106kb on average.Phenotypic analyses showed that mutations in two heavy metal transporter genes, HMA2S and HMA4T, led to reduced accumulation of cadmium and zinc, which was confirmed independently using CRISPR/Cas9 to generate knockout mutants. Our results demonstrate that this powerful TILLING platform(available at http://www.croptilling.org)can be used in tobacco to facilitate functional genomics applications.     

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.     

An experimental study of vascular dynamics by an acceleration plethysmogram using artificial circulation devices

Plethysmogram has been widely known as a conventional non-invasive simple method to obtain information on peripheral circulatory kinetics. We made a quantitative assessment of the relationships between the various circulatory parameters, using the simple conventional measurement method of treating acceleration plethysmograms (the second derivatives of digital plethysmograms) as indicators of peripheral circulation kinetics. We designed a prototype model peripheral circulatory circuit, using an artificial heart, for the purpose of clarifying the relationship between physical factors and plethysmograms. In our models of the peripheral circulatory system, we made use of various types of matching silicon tubes, as well as canine carotid arteries, as substitutes for human arteries. We evaluated the mechanical characteristics, such as the pressure and volume characteristics of the silicon tubes and canine carotid arteries. Plethysmogram alterations were measured using a photoelectric digital plethysmogram. When we examined the acceleration plethysmogram b/a values, which indicate blood vessel extensibility and hardness, and the d/a values, which we were able to use as an index of peripheral circulatory kinetics, it was clear from out model testing that canine carotid arteries displayed b/a values that were closest to those found in the human fingertip; among artificial tubes, the closest was a tube with a diameter of 4 mm (0.18 mm in thickness). The b/a values of all types of tubes declined when the compliance of the arterial system was increased, and it was confirmed through model testing that b/a values are an indicator of blood vessel extensibility.