Identification of relevant properties for epitopes detection using a regression model

A B-cell epitope is a part of an antigen that is recognized by a specific antibody or B-cell receptor. Detecting the immunogenic region of the antigen is useful in numerous immunodetection and immunotherapeutics applications. The aim of this paper is to find relevant properties to discriminate the location of potential epitopes from the rest of the protein surface. The most relevant properties, identified using two evaluation approaches, are the geometric properties, followed by the conservation score and some chemical properties, such as the proportion of glycine. The selected properties are used in a patch-based epitope localization method including a Single-Layer Perceptron for regression. The output of this Single-Layer Perceptron is used to construct a probability map on the antigen surface. The predictive performances of the method are assessed by computing the AUC using cross validation on two benchmark data sets and by computing the AUC and the precision for a third independent test set.     

Emergence,therefore antireductionism? A critique of emergent antireductionism

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims.     

Ice shaping properties, similar to that of antifreeze proteins, of a zirconium acetate complex

The control of the growth morphologies of ice crystals is a critical issue in fields as diverse as biomineralization, medicine, biology, civil or food engineering. Such control can be achieved through the ice-shaping properties of specific compounds. The development of synthetic ice-shaping compounds is inspired by the natural occurrence of such properties exhibited by antifreeze proteins. We reveal how a particular zirconium acetate complex is exhibiting ice-shaping properties very similar to that of antifreeze proteins, albeit being a radically different compound. We use these properties as a bioinspired approach to template unique faceted pores in cellular materials. These results suggest that ice-structuring properties are not exclusive to long organic molecules and should broaden the field of investigations and applications of such substances.     

In vivo liver tissue mechanical properties by Transient Elastography: comparison with Dynamic Mechanical Analysis

Understanding the mechanical properties of human liver is one of the most critical aspects of its numerical modeling for medical applications or impact biomechanics. Generally, model constitutive laws come from in vitro data. However, the elastic properties of liver may change significantly after death and with time. Furthermore, in vitro liver elastic properties reported in the literature have often not been compared quantitatively with in vivo liver mechanical properties on the same organ. In this study, both steps are investigated on porcine liver. The elastic property of the porcine liver, given by the shear modulus G, was measured by both Transient Elastography (TE) and Dynamic Mechanical Analysis (DMA). Shear modulus measurements were realized on in vivo and in vitro liver to compare the TE and DMA methods and to study the influence of testing conditions on the liver viscoelastic properties. In vitro results show that elastic properties obtained by TE and DMA are in agreement. Liver tissue in the frequency range from 0.1 to 4 Hz can be modeled by a two-mode relaxation model. Furthermore, results show that the liver is homogeneous, isotropic and more elastic than viscous. Finally, it is shown in this study that viscoelastic properties obtained by TE and DMA change significantly with post mortem time and with the boundary conditions.     

Micromechanical understanding of the cell-wall structure

For improving properties of pulp fibres, a better understanding of the relationships between its macroscopic mechanical properties, fibre ultrastructure, and properties of the wood polymers is important. This paper discusses such relations between elastic properties of fibres, their matrix structure and the wood polymer elastic constants. It is argued that an orientation of all of the wood polymers in the direction of the cellulose microfibrils is most likely. The elastic longitudinal modulus of cellulose is well described by the value of 134 GPa dominating the longitudinal fibre properties. In the transverse direction the amorphous polymers play a more important role.     

Dynamics in bacterial surface properties of a natural bacterial community in the coastal North Sea during a spring phytoplankton bloom

The hydrophilic and hydrophobic properties of single cells of natural bacterioplankton communities were determined using a recently developed staining method combined with confocal laser scanning microscopy and advanced image analysis. On an average, about 50% of the bacterial cell area was covered by hydrophobic and only 16% by hydrophilic properties, while about 72% was covered by the genome. However, the size of these properties was independent of the bacterial cell size. Bacterial hydrophobicity was positively correlated with ambient NH(4)(+) concentrations and negatively correlated with overall bacterial abundance. The expression of hydrophilicity was more dynamic. Over the spring phytoplankton bloom, the bacterioplankton ratio(phil/phob) repeatedly reached highest values shortly before peaks in bacterioplankton abundance were observed, indicating a direct and fast response of bacterial surface properties, especially hydrophilicity, to changing environmental conditions. Compared to bacterial strains, recently studied with the same method, cells of marine bacterioplankton communities are much smaller and less frequently covered by hydrophobic or hydrophilic properties. While the percentage area covered by the genome is essentially the same, the percentage area covered by hydrophobic or hydrophilic properties is much smaller.     

Dielectric measurements for the design of an electromagnetic rewarming system

The work described in this paper is intended to provide a basis for the design of a controlled rewarming system for cryopreserved tissues and organs using electromagnetic energy. For rapid rewarming (say, greater than 10 degrees C/min), the temperature distribution in the organ is effectively determined by the uniformity (or otherwise) of the power deposition, which is in turn controlled by the electrical properties of the perfused tissue. In this contribution, we describe the measurement system we have used to characterize the electrical properties of perfusates and perfused rabbit kidney tissue from -30 to +20 degrees C. Measurements have been made on three perfusates using an open-ended coaxial probe sensor over a continuous range of radio and microwave frequencies covering 50 MHz to 2.6 GHz. Results show that the behavior of the electrical properties with increasing temperature is unfavorable at either end of the frequency range investigated--either the power absorption has a positive temperature coefficient or the penetration depth is too shallow. However, there is a compromise frequency range, determined in part by the perfusate composition, where these factors are much less serious. In this frequency range, the electrical properties of the perfused tissue are dominated by the properties of the perfusate. Modifications to the perfusate composition, e.g., reducing the concentration of electrolytes by adding sucrose, can further improve the temperature dependence of the electrical properties.     

Evaluation of Muscle Function of the Extensor Digitorum Longus Muscle Ex vivo and Tibialis Anterior Muscle In situ in Mice

Body movements are mainly provided by mechanical function of skeletal muscle. Skeletal muscle is composed of numerous bundles of myofibers that are sheathed by intramuscular connective tissues. Each myofiber contains many myofibrils that run longitudinally along the length of the myofiber. Myofibrils are the contractile apparatus of muscle and they are composed of repeated contractile units known as sarcomeres. A sarcomere unit contains actin and myosin filaments that are spaced by the Z discs and titin protein. Mechanical function of skeletal muscle is defined by the contractile and passive properties of muscle. The contractile properties are used to characterize the amount of force generated during muscle contraction, time of force generation and time of muscle relaxation. Any factor that affects muscle contraction (such as interaction between actin and myosin filaments, homeostasis of calcium, ATP/ADP ratio, etc.) influences the contractile properties. The passive properties refer to the elastic and viscous properties (stiffness and viscosity) of the muscle in the absence of contraction. These properties are determined by the extracellular and the intracellular structural components (such as titin) and connective tissues (mainly collagen) ^1-2. The contractile and passive properties are two inseparable aspects of muscle function. For example, elbow flexion is accomplished by contraction of muscles in the anterior compartment of the upper arm and passive stretch of muscles in the posterior compartment of the upper arm. To truly understand muscle function, both contractile and passive properties should be studied.The contractile and/or passive mechanical properties of muscle are often compromised in muscle diseases. A good example is Duchenne muscular dystrophy (DMD), a severe muscle wasting disease caused by dystrophin deficiency ³. Dystrophin is a cytoskeletal protein that stabilizes the muscle cell membrane (sarcolemma) during muscle contraction ⁴. In the absence of dystrophin, the sarcolemma is damaged by the shearing force generated during force transmission. This membrane tearing initiates a chain reaction which leads to muscle cell death and loss of contractile machinery. As a consequence, muscle force is reduced and dead myofibers are replaced by fibrotic tissues ⁵. This later change increases muscle stiffness ⁶. Accurate measurement of these changes provides important guide to evaluate disease progression and to determine therapeutic efficacy of novel gene/cell/pharmacological interventions. Here, we present two methods to evaluate both contractile and passive mechanical properties of the extensor digitorum longus (EDL) muscle and the contractile properties of the tibialis anterior (TA) muscle.     

Assessing Micromechanical Properties of Cells with Atomic Force Microscopy: Importance of the Contact Point

Mechanical properties are obtainable from atomic force microscopy (AFM) indentation force–depth curves, which are calculated from relationships between tip deflection and cantilever position, i.e. deflection curves. Indentation depth is the difference between tip deflections on a rigid and a soft material for the same amount of cantilever advancement, after contact is made. Since the contact point cannot be unequivocally identified from experimental data, there is some uncertainty in estimating material properties. Using simulations, this study examines some important issues related to the influence of contact point identification on estimated material properties. Simulations for linear materials using a typical stiffness for an AFM cantilever demonstrate that certain portions of the post-contact region of deflection curves for soft and very stiff materials can be approximated by quadratic and linear functions, respectively. Based on these findings, we first develop and verify an objective, automatic method to identify the contact point for materials with linear properties. We then assess the effect of misidentifying the contact point, with and without noise. If the contact point is missed by <50 nm, material properties for small indentations are erroneous but the error decreases asymptotically beyond 200 nm of indentation and the correct estimate of material stiffness is obtained. If the contact point is missed by >100 nm, however, the true material properties cannot be estimated accurately. Noise adds to uncertainty in material properties at small indentations but the combined effect of missing the contact point and noise is dominated by the former. Even though the algorithm was developed for linear materials, it is also suitable for certain nonlinear materials making it more generally applicable.     

Effects of blocking integrin β1 and N-cadherin cellular interactions on mechanical properties of vascular smooth muscle cells

Experimental measurements of cellular mechanical properties have shown large variability in whole-cell mechanical properties between cells from a single population. This heterogeneity has been observed in many cell populations and with several measurement techniques but the sources are not yet fully understood. Cell mechanical properties are directly related to the composition and organization of the cytoskeleton, which is physically coupled to neighboring cells through adherens junctions and to underlying matrix through focal adhesion complexes. This high level of heterogeneity may be attributed to varying cellular interactions throughout the sample. We tested the effect of cell-cell and cell-matrix interactions on the mechanical properties of vascular smooth muscle cells (VSMCs) in culture by using antibodies to block N-cadherin and integrin β1 interactions. VSMCs were cultured on substrates of varying stiffness with and without tension. Under each of these conditions, cellular mechanical properties were characterized by performing atomic force microscopy (AFM) and cellular structure was analyzed through immunofluorescence imaging. As expected, VSMC mechanical properties were greatly affected by the underlying culture substrate and applied tension. Interestingly, the cell-to-cell variation in mechanical properties within each sample decreased significantly in the antibody conditions. Thus, the cells grown with blocking antibodies were more homogeneous in their mechanical properties on both glass and soft substrates. This suggests that diversified adhesion binding between cells and the ECM is responsible for a significant amount of mechanical heterogeneity that is observed in 2D cell culture studies.     

Exopolysaccharides produced by Lactobacillus plantarum: technological properties,biological activity,and potential application in the food industry

Some lactic acid bacteria are capable of producing capsular or extracellular polysaccharides, with desirable technological properties and biological activities. Such polysaccharides produced by lactic acid bacteria are called exopolysaccharides and can be used to alter rheological properties, acting in processes involving viscosity, emulsification, and flocculation, among others. They may also be involved in prebiotic, probiotic, and biological activities, as well as having potential application in the food industry. In this mini-review, the objectives were to present some beneficial properties of exopolysaccharides (EPS) produced by Lactobacillus plantarum that have not been commercially explored. For that, the article focused to summarize revision of current publications within the following topics: (1) rheological properties, (2) prebiotic properties, (3) biological activities, and (4) potential application in the food industry. EPS produced by Lb. plantarum can be used as gelling agent, emulsifier, or stabilizer for food products. The glucan nature of the produced EPS enhances probiotic properties of this LAB species. Lactobacillus plantarum EPS has antioxidant, antibiofilm, and antitumor activities. Finally, there is an improvement in texture of fermented food products where Lb. plantarum is used as starter culture which is related to EPS production in situ. Therefore, EPS produced by Lb. plantarum have important and desirable properties to be explored for several applications, including health and food areas.     

New field of insect science: Research on the use of insect properties

In recent years, research on “insect properties” has been attracting much attention for industrial applications of insect technology. This is a new field of research that attempts to analyze specific physiological properties of insects to develop technology for helping humankind. The term “insect properties” has been used to refer to “specific biological functions of insects” since around 1986, and it is now widely accepted in Japan. From 1996, the National Institute of Sericultural and Entomological Science (NISES) promoted “Research for utilization of insect properties” as a “Center of Excellence (COE)” project funded by the Science and Technology Agency. At this point, a new research field called “Research for utilization of insect properties” was initiated, and this led to the recognition of this field by the academic community. In the 21st century, remarkable results, including the development of transgenic silkworms and the full decoding of the silkworm genome, have been achieved. It is expected that this advanced technology will be a powerful tool for progress of research on the use of insect properties. This review presents an overview of the current state of research on use of insect properties as a new technology.     

Effects of Phosphate Residues on the Excellent Emulsifying Properties of Phosphoglycoprotein Phosvitin

The effects of phosphate residues in phosvitin on its emulsifying properties were investigated. The emulsifying properties, especially the emulsion stability, of phosvitin were much superior to those of bovine serum albumin which is an excellent emulsifier. The emulsifying activity and emulsion stability of phosvitin were greatly decreased by the partial removal of phosphate with phosphatase and by the complete removal of phosphate with alkaline treatment. In addition, the emulsifying properties were decreased by the blocking of phosphate in phosvitin with calcium ion. These results suggest that the electrostatic repulsive force of phosphate in phosvitin significantly affects its emulsifying properties.     

低温淀粉酶菌株C2的分离鉴定及其产低温淀粉酶的酶学性质

获得低温淀粉酶高产菌株,确定该菌株所产淀粉酶的酶学性质.从大黑山(大连)污泥中筛选菌株,通过菌株的形态特征、生理生化和16S rDNA序列鉴定确定其种属,对其酶学性质进行初步研究.获得1株低温淀粉酶高产菌株C2,经鉴定其为微小杆菌属,C2所产低温淀粉酶最适反应温度为25℃,酶的热稳定性比较差,最适pH为7.5,Ca2+和Fe2+对该酶有激活作用,Cu2+、Ni2+、Go2+等抑制酶活性.经薄层层析(TLC)鉴定酶解产物为葡萄糖,说明该菌株具有产生低温淀粉糖化酶的能力.菌株C2所产淀粉酶符合低温淀粉酶性质,值得进一步研究.     

Capturing the bursting dynamics of a two-cell inhibitory network using a one-dimensional map

Out-of-phase bursting is a functionally important behavior displayed by central pattern generators and other neural circuits. Understanding this complex activity requires the knowledge of the interplay between the intrinsic cell properties and the properties of synaptic coupling between the cells. Here we describe a simple method that allows us to investigate the existence and stability of anti-phase bursting solutions in a network of two spiking neurons, each possessing a T-type calcium current and coupled by reciprocal inhibition. We derive a one-dimensional map which fully characterizes the genesis and regulation of anti-phase bursting arising from the interaction of the T-current properties with the properties of synaptic inhibition. This map is the burst length return map formed as the composition of two distinct one-dimensional maps that are each regulated by a different set of model parameters. Although each map is constructed using the properties of a single isolated model neuron, the composition of the two maps accurately captures the behavior of the full network. We analyze the parameter sensitivity of these maps to determine the influence of both the intrinsic cell properties and the synaptic properties on the burst length, and to find the conditions under which multistability of several bursting solutions is achieved. Although the derivation of the map relies on a number of simplifying assumptions, we discuss how the principle features of this dimensional reduction method could be extended to more realistic model networks. Action Editor: John Rinzel     

A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics

Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary.     

A chimeric glutamate receptor subunit: discrete changes modify the properties of the channel.

GluR1 and GluR2 are two highly homologous subunits of the glutamate AMPA receptor but with different functional properties. In ligand gated channels the transmembrane domain II is thought to form the wall of the ionic pore and determine the electrical properties. A chimeric AMPA receptor subunit was constructed by replacing the region comprising transmembrane domains I and II in GluR1 by the corresponding region of GluR2. Alone or forming an heteromer with GluR1, the resulting chimera has the properties of GluR2. Sequence comparison suggests that an arginine at position 600 in the chimera instead of a glutamine in GluR1 is responsible for these properties.     

Micro- and macrorheology of jellyfish extracellular matrix

Mechanical properties of the extracellular matrix (ECM) play a key role in tissue organization and morphogenesis. Rheological properties of jellyfish ECM (mesoglea) were measured in vivo at the cellular scale by passive microrheology techniques: microbeads were injected in jellyfish ECM and their Brownian motion was recorded to determine the mechanical properties of the surrounding medium. Microrheology results were compared with macrorheological measurements performed with a shear rheometer on slices of jellyfish mesoglea. We found that the ECM behaved as a viscoelastic gel at the macroscopic scale and as a much softer and heterogeneous viscoelastic structure at the microscopic scale. The fibrous architecture of the mesoglea, as observed by differential interference contrast and scanning electron microscopy, was in accord with these scale-dependent mechanical properties. Furthermore, the evolution of the mechanical properties of the ECM during aging was investigated by measuring microrheological properties at different jellyfish sizes. We measured that the ECM in adult jellyfish was locally stiffer than in juvenile ones. We argue that this stiffening is a consequence of local aggregations of fibers occurring gradually during aging of the jellyfish mesoglea and is enhanced by repetitive muscular contractions of the jellyfish.     

Active and passive properties of carotid arteries]

A mathematical model of carotid arteries is constructed from the known experimental data. Passive properties of the vascular wall are characterized by an alternating module of elasticity, the active ones by the specific power of muscle contraction. Its maximum value (0,023 n/m-3) is shown to be reached with intravascular pressure 190 mm Hg. The dependence of inner radius on the power of muscle contraction is studied at different values of intravascular pressure. It is shown that theactive properties of carotid arteries are essentially determined by their passive properties and depend on the stretching of the vessel wall.