Biobanking

Biobanks, more formally known as biological resource centers (BRCs), form an “unsung” yet critical component of the infrastructures for scientific research, industry and conservation, without which much of the current scientific activity involving microbial cultures and cell-lines would be effectively impossible. BRCs are de facto depositories of “biological standards” holding taxonomic and other reference strains on which much of the associated published science and industrial standards are built and upon which some significant international commercial and ethical issues rely. The establishment and maintenance of BRCs is a knowledge- and skill-rich activity that in particular requires careful attention to the implementation of reliable preservation technologies and appropriate quality assurance to ensure that recovered cultures and other biological materials perform in the same way as the originally isolated culture or material. There are many types of BRC, which vary both in the kinds of material they hold and in their functional role. All BRCs are expected to provide materials and information of an appropriate quality for their intended use and work to standards relevant to those applications. There are important industrial, biomedical, and conservation issues that can only be addressed through effective and efficient operation of BRCs in the long term. This requires a high degree of expertise in the maintenance and management of collections of biological materials at ultra-low temperatures, or as freeze-dried material, to secure their long-term integrity and relevance for future research, development, and conservation.     

Make Histri: reconstructing the exchange history of bacterial and archaeal type strains

Each transfer of a microbial strain between a Biological Resource Center (BRC) and an individual researcher or another BRC imposes a risk of contamination or human error. Such artifacts jeopardize the quality of scientific results. In order to trace back possible scientific discrepancies that can be linked to failure of authenticity of the biological material involved, we launched the 'Make Histri' project that aims at reconstructing the exchange history ('Histri') of all bacterial and archaeal type strains as can be deduced from the information contained in BRC online catalogs. A Histri, visualized as a rooted tree, contains all known strain numbers attributed to the various cultures of a given strain, annotated with additional information about each transfer of microbial material.     

Photoactivation and conformational gating for manganese binding and oxidation in bacterial reaction centers

The influence of illumination history of native bacterial reaction centers (BRCs) on the ability of binding and photo-induced oxidation of manganous ions was investigated in the pH range between 8.0 and 9.4. Binding of manganous ions to a buried site required 6 to 11-fold longer incubation periods, depending on the pH, in dark-adapted BRCs than in BRCs that were previously illuminated prior to manganese binding. The intrinsic electron transfer from the bound manganese ion to the photo-oxidized primary electron donor was found to be limited by a 2 to 5-fold slower precursor conformational step in the dark-adapted samples for the same pH range. The conformational gating could be eliminated by photoactivation, namely if the BRCs were illuminated prior to binding. Unlike in Photosystem II, photoactivation in BRCs did not involve cluster assembly. Photoactivation with manganese already bound was only possible at elevated detergent concentration. In addition, also exclusively in dark-adapted BRCs, a marked breaking point in the Arrhenius-plot was discovered around 15 °C at pH 9.4 indicating a change in the reaction mechanism, most likely caused by the change of orientation of the 2-acetyl group of the inactive bacteriochlorophyll monomer located near the manganese binding site.     

Requirements for comparing the performance of finite element models of biological structures

The widespread availability of three-dimensional imaging and computational power has fostered a rapid increase in the number of biologists using finite element analysis (FEA) to investigate the mechanical function of living and extinct organisms. The inevitable rise of studies that compare finite element models brings to the fore two critical questions about how such comparative analyses can and should be conducted: (1) what metrics are appropriate for assessing the performance of biological structures using finite element modeling? and, (2) how can performance be compared such that the effects of size and shape are disentangled? With respect to performance, we argue that energy efficiency is a reasonable optimality criterion for biological structures and we show that the total strain energy (a measure of work expended deforming a structure) is a robust metric for comparing the mechanical efficiency of structures modeled with finite elements. Results of finite element analyses can be interpreted with confidence when model input parameters (muscle forces, detailed material properties) and/or output parameters (reaction forces, strains) are well-documented by studies of living animals. However, many researchers wish to compare species for which these input and validation data are difficult or impossible to acquire. In these cases, researchers can still compare the performance of structures that differ in shape if variation in size is controlled. We offer a theoretical framework and empirical data demonstrating that scaling finite element models to equal force: surface area ratios removes the effects of model size and provides a comparison of stress-strength performance based solely on shape. Further, models scaled to have equal applied force:volume ratios provide the basis for strain energy comparison. Thus, although finite element analyses of biological structures should be validated experimentally whenever possible, this study demonstrates that the relative performance of un-validated models can be compared so long as they are scaled properly.     

Stability of short sequence repeats and their application for the characterization of Erwinia amylovora strains

A motif of eight nucleotides (GAATTACA) reiterated 3 to 15 times within the PstI fragment of the pEa29 plasmid was found in Erwinia amylovora strains representing a valuable typing method for this pathogen. The stability of short sequence DNA repeat (SSR) numbers was investigated to determine the suitability of this marker for strain differentiation. The number of SSR units was found to be stable under laboratory and certain stress conditions. This meets the requirements for a suitable genetic marker that should be stable upon cultivation of strains. Therefore, this SSR marker was used for strain differentiation from SSR-3 to SSR-15 and a large number of E. amylovora strains from Austria was screened for their SSR numbers for epidemiological identification purposes. Traceability was possible if strains had very high or very low SSR numbers.     

Experimental investigation of the elastic-plastic deformation of mineralized lobster cuticle by digital image correlation

This study presents a novel experimental approach to the characterization of the deformation of a mineralized biological composite using arthropod cuticle as a model material. By performing tensile tests combined with a detailed strain analysis via digital image correlation, the elastic-plastic deformation behavior of the endocuticle of the American lobster Homarus americanus is examined. The test specimens originate from the pincher and crusher claws. For evaluating the effect of moisture on the deformation behavior, the samples are tested both in dry and in wet state. Sample characterization using the digital image correlation method requires a stochastic spot pattern on the sample surface. Digital images are then taken at subsequent deformation stages during the mechanical test. These images are used to calculate the displacement, the displacement gradient, and the strain fields via pattern correlation. The method is applied both, at a global scale to measure with high precision the stress-strain behavior of the bulk cuticle and at a microscopic scale to reveal strain heterogeneity, strain patterning, and strain localization phenomena.     

Laser-guided direct writing for applications in biotechnology.

Laser-induced optical forces can be used to guide and deposit 100 nm - 10 microm-diameter particles onto solid surfaces in a process we call 'laser-guided direct writing'. Nearly any particulate material, including both biological and electronic materials, can be manipulated and deposited on surfaces with micrometer accuracy. Potential applications include three-dimensional cell patterning for tissue engineering, hybrid biological-electronic-device construction, and biochip-array fabrication.     

一株红假单胞菌的分离及对Cu2+的去除

【背景】重金属污染对环境和人类的健康构成了重大威胁,因此,重金属污染的治理迫在眉睫。生物治理因成本低、处理效果好和无二次污染等优点,在处理重金属污染时被优先选择。【目的】从辽河入海口深13 m的水体中,利用紫色非硫细菌富集培养基筛选产色素能力强并对高浓度Cu~(2+)有高效去除能力的菌株。【方法】采用形态学、生理生化特性和分子生物学方法鉴定菌种;采用二乙基二硫代氨基甲酸钠分光光度法测定Cu~(2+)的含量。【结果】鉴定菌株为红假单胞菌属,将其命名为Rhodopseudomonas sp. gh32。菌株gh32的最适生长温度和最适pH分别为30°C和7.0,其在pH 5.0-10.0范围内可正常生长,在3 mmol/L的CuSO4溶液中能够正常生长,能利用葡萄糖、甘露糖和果糖等单糖和硫化氢。菌株gh32在24h内对Cu~(2+)的去除率均在99%以上,处理能力为1 331 g/g干菌重或167.6 g/g湿菌重。【结论】菌株gh32对Cu~(2+)具有较强的耐受性和很好的去除效果,是治理含Cu~(2+)废水的潜力菌株。本研究为生物治理重金属废水提供了支持。     

Estimating axonal strain and failure following white matter stretch using contactin-associated protein as a fiduciary marker

Axonal injury occurs during trauma when tissue-scale loads are transferred to individual axons. Computational models are used to understand this transfer and predict the circumstances that cause injury. However, these findings are limited by a lack of validating experimental work examining the mechanics of axons in their in situ state. As a first step towards validation for dynamic stretch, we use contactin-associated protein (Caspr), expressed at the nodes of Ranvier, as a fiduciary marker of quasistatic axonal stretch. We measured changes in the distance between immunolabled Caspr pairs along axons as a function of tissue-level stretch in chick embryo spinal cords harvested from different developmental periods. We then identified and characterized broken axons and adapted a kinematic model published previously by our group (Singh et al., 2015) to estimate average strain thresholds for axon mechanical failure. The distance between Caspr pairs increased with stretch, though not as much as predicted by simple continuum mechanics. For equivalent tissue stretch, greater numbers of broken axons were found at later stages of development. In adapting our kinematic model to predict a breaking threshold strain, we found that breaking thresholds decrease with development stage. When thresholds were split and classified based on kinematic behavior, non-affine, uncoupled axons had higher strain thresholds than affine, coupled axons, corroborating thresholds predicted from in vitro and in vivo preparations. These results provide a valuable launching point for generating more accurate multi-scale models in primary central nervous system injury.     

A poroviscoelastic description of fibrin gels

The mechanical induction of specific cell phenotypes can only be properly controlled if the local stimuli applied to the cells are known as a function of the external applied loads. Finite element analysis of the cell carriers would be one method to calculate these local conditions. Furthermore, the constitutive model of the construct material should be able to describe mechanical events known to be responsible for cell stimulation, such as interstitial fluid flow. The aim of this study was to define a biphasic constitutive model for fibrin, a natural hydrogel often used for tissue engineering but not yet thoroughly characterized. Large strain poroelastic and poroviscoelastic constitutive equations were implemented into a finite element model of a fibrin gel. The parameter values for both formulations were found by either analytically solving equivalent low strain equations, or by optimizing directly the large strain equations based on experimental stress relaxation data. No poroelastic parameters that satisfactorily described the fibrin carrier behaviour could be found, suggesting that network viscoelasticity and fluid-flow time-dependent behaviour must be separately accounted for. It was demonstrated that fibrin can be described as a poroviscoelastic material, but a large strain characterization of the parameter values was necessary. The analytical resolution of the low strain poroviscoelastic equations was, however, accurate enough to serve as a reliable initial condition for further optimization of the parameter values with the large strain formulation.     

Comparison of bacterial reaction centers and photosystem II

In photosynthetic organisms, the utilization of solar energy to drive electron and proton transfer reactions across membranes is performed by pigment-protein complexes including bacterial reaction centers (BRCs) and photosystem II. The well-characterized BRC has served as a structural and functional model for the evolutionarily-related photosystem II for many years. Even though these complexes transfer electrons and protons across cell membranes in analogous manners, they utilize different secondary electron donors. Photosystem II has the unique ability to abstract electrons from water, while BRCs use molecules with much lower potentials as electron donors. This article compares the two complexes and reviews the factors that give rise to the functional differences. Also discussed are the modifications that have been performed on BRCs so that they perform reactions, such as amino acid and metal oxidation, which occur in photosystem II.     

A frame-invariant formulation of Fung elasticity

Fung elasticity refers to the hyperelasticity constitutive relation proposed by Fung and co-workers for describing the pseudo-elastic behavior of biological soft tissues undergoing finite deformation. A frame-invariant formulation of Fung elasticity is provided for material symmetries ranging from orthotropy to isotropy, which uses Lamé-like material constants. In the orthotropic case, three orthonormal vectors are used to define mutually orthogonal planes of symmetry and associated texture tensors. The strain energy density is then formulated as an isotropic function of the Lagrangian strain and texture tensors. The cases of isotropy and transverse isotropy are derived from the orthotropic case. Formulations are provided for both material and spatial frames. These formulations are suitable for implementation into finite element codes. It is also shown that the strain energy function can be naturally uncoupled into a dilatational and a distortional part, to facilitate the computational implementation of incompressibility.     

Static indentation of anisotropic biomaterials using axially asymmetric indenters--a computational study

Indentation has historically been used by biomechanicians to extract the small strain elastic or viscoelastic properties of biological tissues. Because of the axisymmetry of indenters used in these studies however, analysis of the results requires the assumption of material isotropy and often yields an "effective" elastic modulus. Since most biological tissues such as bone and myocardium are known to be anisotropic, the use of conventional indentation techniques for estimating material properties is therefore limited. The feasibility of using an axially asymmetric indenter to determine material directions and in-plane material properties for anisotropic tissue is explored here using finite element analysis. The load versus displacement curves as would be measured by an indenter depend on the orientation of the indenter cross section relative to the in-plane material axes, thus suggesting a method for determining the underlying material directions. Additionally, the stiffness of the tissue response to indentation is sensitive to the values of the in-plane anisotropic material properties and prestretches, and thus test results can be used to back out relevant constitutive parameters.     

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.     

Tuning the redox potential of the primary electron donor in bacterial reaction centers by manganese binding and light-induced structural changes

The influence of transition metal binding on the charge storage ability of native bacterial reaction centers (BRCs) was investigated. Binding of manganous ions uniquely prevented the light-induced conformational changes that would yield to long lifetimes of the charge separated state and the drop of the redox potential of the primary electron donor (P). The lifetimes of the stable charge pair in the terminal conformations were shortened by 50-fold and 7-fold upon manganous and cupric ion binding, respectively. Nickel and zinc binding had only marginal effects. Binding of manganese not only prevented the drop of the potential of P/P⁺ but also elevated it by up to 117 mV depending on where the metal was binding. With variable conditions, facilitating either manganese binding or light-induced structural changes a controlled tuning of the potential of P/P⁺ in multiple steps was demonstrated in a range of ~200 mV without the need of a mutation or synthesis. Under the selected conditions, manganese binding was achieved without its photochemical oxidation thus, the energized but still native BRCs can be utilized in photochemistry that is not reachable with regular BRCs. A 42 Å long hydrophobic tunnel was identified that became obstructed upon manganese binding and its likely role is to deliver protons from the hydrophobic core to the surface during conformational changes.     

一株高产黑色素细菌的分离及鉴定*

从武汉东湖中分离出一株高产胞外黑色素的细菌(BFHM2002)。BFHM2002具有产黑色素速度快,产量高且不需要酪氨酸诱导等优点;而且经酪氨酸诱导可显提高BF-HM2002胞外黑色素的产量,初步鉴定BFHM2002属坚强芽孢杆菌(Bacillus firmus)。鉴于BFHM2002的产黑色素特性,将成为芽孢杆菌属的一个新的菌种资源。     

Biological verification of heavy ion treatment planning

Chinese hamster ovary (CHO) cells and thermoluminescent detectors (TLD-700) were used for physical and biological verification of heavy ion treatment planning. Experiments were performed in a cylindrical water phantom, in some cases with lung and bone equivalent material in front of the target volume. The results confirm the possibility of using thermoluminescent detectors for a quantitative verification of dose distributions. CHO cells can be used at least for qualitative dose verification. Received: 15 December 1997 / Accepted in revised form: 6 February 1998     

Assessment of intramuscular activation patterns using ultrasound M-mode strain

The intramuscular activation pattern can be connected to the motor unit recruitment strategy of force generation and fatigue resistance. Electromyography has earlier been used in several studies to quantify the spatial inhomogeneity of the muscle activation. We applied ultrasound M-mode strain to study the activation pattern through the tissue deformation. Correlation values of the strain at different force levels were used to quantify the spatial changes in the activation. The assessment was done including the biceps brachii muscle of 8 healthy subjects performing isometric elbow flexion contractions ranging from 0% to 80% of maximum voluntary contraction. The obtained results were repeatable and demonstrated consistent changes of the correlation values during force regulation, in agreement with previously presented EMG-results. Both intra-subject and inter-subject activation patterns of strain were considered along and transverse the fiber direction. The results suggest that ultrasound M-mode strain can be used as a complementary method to study intramuscular activation patterns with high spatial resolution.     

A method for assessing the fit of a constitutive material model to experimental stress–strain data

Higher-order polynomial functions can be used as a constitutive model to represent the mechanical behaviour of biological materials. The goal of this study was to present a method for assessing the fit of a given constitutive three-dimensional material model. Goodness of fit was assessed using multiple parameters including the root mean square error and Hotelling's T ²-test. Specifically, a polynomial model was used to characterise the stress–strain data, varying the number of model terms used (45 combinations of between 3 and 11 terms) and the manner of optimisation used to establish model coefficients (i.e. determining coefficients either by parameterisation of all data simultaneously or averaging coefficients obtained by parameterising individual data trials). This framework for model fitting helps to ensure that a given constitutive formulation provides the best characterisation of biological material mechanics.