How electronic interference can be applied in the research of the structure of small bioobjects and for "fast reading" of nucleotide sequences

A method for the study of the surface of small bioobjects, such as macromolecules and their complexes has been developed. The method is based on the phenomenon of the interference of low-energy electrons. Using the interference, it is possible to construct analogues of holograms for these bioobjects but, as distinct from optical holography, with the spatial restriction at the level of internuclear distances. The method enables one to obtain a set of holograms at different energies of electrons. The information thus obtained can suffice to determine the type of molecular groups located on the suffice of the object being examined. The method can be used, e.g., for the "fast reading" of genetic texts.     

Glucose-sensitive holographic sensors

Holographic sensors for monitoring glucose were fabricated from hydrogel films containing chemical ligands based on phenylboronic acid. The films were transformed into reflection holograms using a diffusion method coupled with exposure to laser light. The diffraction wavelength of the holograms was used to monitor the swelling of the hydrogel film in the presence of glucose. Fully reversible changes in diffraction wavelength were demonstrated, highlighting the potential for using these holograms as glucose sensors.     

Physical simulation of neuronal memory as a mosaic of chemoreceptor and electroreceptor elements of the somato-dendritic membrane

A model of neuronal memory in which recording and reading out are based on scanning of the somato-dendritic membrane is analyzed. The stepwise displacement of excesses of potential relief created by superposition of local postsynaptic potentials on the soma-to-dendritic membrane is used as the scanner. Associative, diagnostic, and dependable (distributive) properties of such a memory, similar to the properties of holograms, are demonstrated.M. I. Kalinin Leningrad Polytechnical Institute. Translated from Neirofiziologiya, Vol. 6, No. 1, pp. 90–98, January–February, 1974.     

Study of binding between protein A and immunoglobulin G using a surface tension probe

Molecular interactions and binding are one of the most important and fundamental properties in the study of biochemical and biomedical systems. The understanding of such interactions and binding among biomolecules forms the basis for the design and processing of many biotechnological applications, such as bioseparation and immunoadsorption. In this study, we present a novel method to probe molecular interactions and binding based on surface tension measurement. This method complements conventional techniques, which are largely based on optical, spectroscopic, fluorescence polarization, chromatographic or atomic force microscopy measurements, by being definite in determining molecular binding ratio and flexible in sample preparation. Both dynamic and equilibrium (or quasi-equilibrium) information on molecular binding can be obtained through dynamic and equilibrium surface tension measurements. For an important pair of biological ligand and ligate, Protein A and immunoglobulin G (IgG), the existence of molecular interactions and the binding ratio of 1:2 have been determined unequivocally with the proposed surface tension method. These results are confirmed/supported by a mass balance calculation and spectrophotometry experiment. In addition, adsorption isotherms for Protein A and IgG separately at the air/water interface have been established with the dynamic surface tension measurements. The results show that the Langmuir isotherm equation can describe the adsorption data satisfactorily for both Protein A and IgG solutions.     

A method for enumeration ot T and B lymphocytes in tissues.

A method for the identification of T and B lymphocytes in tissue specimens is described. A sonication technique results in viable relatively pure lymphocyte populations which are easily classified by their surface markers. This readily reproducible method can become a standard laboratory procedure in the evaluation of disease states which require such information related to the classification of lymphocyte cell origin.     

Changes in dynamics of phase transitions in various liquids by recording of acoustic mechanical impedance of a drying drop

A method of studying multicomponent liquids is proposed, which is based on recording the dynamics of the acoustomechanical impedance of a drop that dries up on the surface of a quartz resonator oscillating with an ultrasound frequency. The magnitude of the acoustomechanical impedance is an integral characteristic of the physical properties of the drop such as viscosity, composition, surface tension, moistening, and inner structure. Using liquids of different types as an example, it was shown that each liquid possesses its individual "portrait", which is determined by the phase transitions. The method can be used for the screening identification of liquids (determining the degree of consistency with the standards) in solving a number of scientific and practical problems, as well as in medicine.     

A universal protocol for photochemical covalent immobilization of intact carbohydrates for the preparation of carbohydrate microarrays

A universal photochemical method has been established for the immobilization of intact carbohydrates and their analogues, and for the fabrication of carbohydrate microarrays. The method features the use of perfluorophenyl azide (PFPA)-modified substrates and the photochemical reaction of surface azido groups with printed carbohydrates. Various aldoses, ketoses, nonreducing sugars such as alditols, and their derivatives can be directly arrayed on the PFPA-modified chips. The lectin-recognition ability of arrayed mannose, glucose, and their oligo- and polysaccharides were confirmed using surface plasmon resonance imaging and laser-induced fluorescence imaging.     

Nonparametric Bayesian estimation of the three-way receiver operating characteristic surface

We describe a nonparametric Bayesian approach for estimating the three-way ROC surface based on mixtures of finite Polya trees (MFPT) priors. Mixtures of finite Polya trees are robust models that can handle nonstandard features in the data. We address the difficulties in modeling continuous diagnostic data with skewness, multimodality, or other nonstandard features, and how parametric approaches can lead to misleading results in such cases. Robust, data-driven inference for the ROC surface and for the volume under the ROC surface is obtained. A simulation study is performed to assess the performance of the proposed method. Methods are applied to data from a magnetic resonance spectroscopy study on human immunodeficiency virus patients.     

Holographic sensors for the detection of bacterial spores

Holographic sensors for the detection of Bacillus species spore germination and vegetative growth are described. Reflection holograms were fabricated using a diffusion method for the distribution of ultra-fine silver bromide grains into pre-formed polymer films, followed by holographic recording using a frequency doubled Nd:YAG (532 nm) laser. Changes in holographic replay wavelength or diffraction intensity were used to characterise the swelling behaviour or structural integrity of a range of holographic matrices in response to various extracellular products of bacterial spore germination and vegetative metabolism. Divalent metal ion-sensitive holograms containing a methacrylated analogue of nitrilotriacetic acid (NTA) as the chelating monomer were successfully used to monitor Ca2+ ions released during B. subtilis spore germination in real-time, which was within minutes of sample addition; the holographic response manifested as a 16 nm blue-shift in diffraction wavelength over the progress of germination. Similarly, pH-sensitive holograms comprising methacrylic acid (MAA) as the ionisable monomer were responsive to changes in pH associated with early vegetative metabolism following germination of B. megaterium spores; a visually perceptible blue-shift in holographic replay wavelength of 75 nm was observed. Casein and starch-based holographic matrices, prepared by co-polymerisation of the appropriate substrate with acrylamide, were used to detect exo-enzymes released during later stages of B. megaterium and B. subtilis vegetative cell growth; holographic responses of both matrices were visible as a reduction in diffraction intensity due to progressive fringe disruption caused by enzymatic cleavage. The combined monitoring of various germination and growth events using the range of aforementioned holographic sensors provides a novel, comprehensive means for the detection of viable bacterial spores.     

Solvophobic forces and molecular surface area changes in drug-biomolecule associations as with actinomycin-deoxyguanosine in a wide range of methanol/water mixtures

A method is given to predict the unitary free energies of complexation between drug-like and nucleoside-like biomolecules in a range of mixed solvent compositions. A stability maximum for the actinomycin (A)-deoxyguanosine (D) complex at 8% MeOH (v/v) in methanol/water mixtures is correctly predicted by the theory in agreement with existing experimental data. The molecular surface areas of A and D exposed to the solvent are found to diminish by 36.4 A(2) upon association. The 'microthermodynamic differential surface tension' of the solvophobic theory obtained for nucleoside-like and organic molecules in contact with MeOH/H2O can be used to predict the solvent effect free energies in other such molecular or biopolymeric associations in solution.     

The "third" dimension in craniofacial surgery

A new method for reconstruction of a three-dimensional surface from a sequence of high-resolution axial CT scans has been developed. This algorithm is realized as a set of computer programs that can operate on commercially available CT scanners or evaluation consoles. The program is both efficient and easy to implement. No operator intervention is required. The images produced simulate photographs of the skull. Frontal, lateral, oblique, bird's eye, worm's eye, and rear views are generated. As with photographs and conventional radiographs, each of these projections uniquely displays specific anatomic details. This method of osseous surface reconstruction is now routinely applied to all patients evaluated for major craniofacial reconstruction at our institution. The images are useful in defining aberrant anatomy, planning surgical procedures, and evaluating the results of such operations. This method replaces an inexact concept in the surgeon's imagination with a three-dimensional image of the craniofacial skeleton.     

噬菌体表面呈现技术研究进展

噬菌体表面呈现技术是1985年建立的一种将外源基因表达呈现在噬菌体颗粒表面的方法,可用于建立随机多肽文库、抗体文库等。经特定配基的筛选,可获得与其特异结合的配体分子。通过改构,还可将cDNA产物表达于噬菌体颗粒的尾部构建cDNA文库。SIP技术通过将配体和配基分别与基因Ⅲ蛋白的C末端和N末端融合表达,基因Ⅲ的C-末端参与噬菌体颗粒的组装,配基与配体的结合能够重建基因Ⅲ蛋白的功能,才能形成有感染能力的噬菌体,这样就大大提高了筛选效率。     

Towards the real-time monitoring of glucose in tear fluid: holographic glucose sensors with reduced interference from lactate and pH

Glucose-selective holographic sensors were fabricated from unique tetrahedral 2-acrylamidophenylboronic acid (2-APB) incorporated with co-monomers poly(ethylene glycol) acrylate (PEG), (3-acrylamidopropyl)trimethylammonium chloride (ATMA) and [2-(acryloyloxy)ethyl]-trimethylammonium chloride (AETA) into thin hydrogel films which were transformed into volume holograms using a diffusion method coupled with holographic recording using a frequency-doubled Nd:YAG laser (532 nm). The results showed that the 2-APB-based holographic sensors contracted upon addition of glucose due to the formation of a 2:1 complex between the tetrahedral 2-APB and glucose. More significantly, the 2-APB-based holographic sensors had greatly reduced lactate dependence and a hugely reduced pH effect over the physiological range of pH. These features are vital for development of contact lens-based glucose sensor, where the pH variability is greater (pH 5.8-7.8) and the lactate concentration is substantially higher than in blood. Furthermore, the 2-APB-based holographic sensors also displayed fast response to glucose. The successful union of holograms and the tetrahedral 2-APB receptor for glucose detection in artificial tear fluid is also demonstrated. This new type of holographic sensors responding to glucose with features of minor pH effect and negligible interference from lactate is applicable to the detection of glucose concentrations in tear fluid for the management of diabetes.     

Analysis of surface growth in shoot apices

A salient feature of shoot meristem growth is the maintenance of distinct anatomical and morphological features despite a continuous flux of cells. To investigate how meristem organization is self-perpetuated, we developed a protocol for the analysis of meristem growth in 3-D. Our protocol uses a non-destructive replica method to follow the pattern of cell expansion and cell divisions on the meristem surface over several days. Algorithms to reconstruct the meristem surface and compute its curvature and rate of extension were implemented. We applied this approach to the shoot apical meristem of Anagallis arvensis and showed that a subcellular resolution of extension rates can be achieved. This is the first detailed quantitative analysis of meristem geometry and surface expansion in 3-D. This new approach will be useful to connect cellular activities such as cell expansion, cell division, and differential gene expression with overall meristem morphogenesis.     

Compensation for loss of ligand activity in surface plasmon resonance experiments

The determination of equilibrium binding constants is an important aspect of the analysis of protein-protein interactions. In recent years surface plasmon resonance experiments (e.g., with a BIAcore instrument) have provided a valuable experimental approach to determining such constants. The standard method is based on measuring amounts of analyte bound at equilibrium for different analyte concentrations. During the course of a typical surface plasmon resonance experiment the measured equilibrium levels for a given analyte concentration often decrease. This appears to be due to a loss of activity of the protein coupled to the sensor chip or other phenomena. The loss in signal can lead to an erroneous determination of the equilibrium constant. A data analysis approach is introduced that aims to compensate for the loss of activity so that its influence on the results of the experiments is reduced.     

Glycopeptide Capture for Cell Surface Proteomics

Cell surface proteins, including extracellular matrix proteins, participate in all major cellular processes and functions, such as growth, differentiation, and proliferation. A comprehensive characterization of these proteins provides rich information for biomarker discovery, cell-type identification, and drug-target selection, as well as helping to advance our understanding of cellular biology and physiology. Surface proteins, however, pose significant analytical challenges, because of their inherently low abundance, high hydrophobicity, and heavy post-translational modifications. Taking advantage of the prevalent glycosylation on surface proteins, we introduce here a high-throughput glycopeptide-capture approach that integrates the advantages of several existing N-glycoproteomics means. Our method can enrich the glycopeptides derived from surface proteins and remove their glycans for facile proteomics using LC-MS. The resolved N-glycoproteome comprises the information of protein identity and quantity as well as their sites of glycosylation. This method has been applied to a series of studies in areas including cancer, stem cells, and drug toxicity. The limitation of the method lies in the low abundance of surface membrane proteins, such that a relatively large quantity of samples is required for this analysis compared to studies centered on cytosolic proteins.     

Modeling rough stenoses by an immersed-boundary method

A pulsatile laminar flow of a viscous, incompressible fluid through a stenosed artery was simulated by an immersed-boundary method. The method allows the use of a simple (rectangular) computational domain in order to simulate a flow around a complex geometry obstacle with surface irregularities (roughness). The influence of the shape and the surface roughness on the flow resistance was explored. The obtained numerical results were validated by comparison with published experimental and numerical results. We show that the surface irregularities have no significant influence on the flow resistance across an obstacle for a physiological range of Reynolds numbers. Notwithstanding, an accurate representation of irregularities allows investigation of the near-wall effects of a realistic flow such as fluid recirculation. We show that a detailed study of flow patterns in the immediate vicinity of the irregular surface can be performed using the immersed boundary method.     

Quantitative phase imaging with scanning holographic microscopy: an experimental assesment

This paper demonstrates experimentally how quantitative phase information can be obtained in scanning holographic microscopy. Scanning holography can operate in both coherent and incoherent modes, simultaneously if desired, with different detector geometries. A spatially integrating detector provides an incoherent hologram of the object's intensity distribution (absorption and/or fluorescence, for example), while a point detector in a conjugate plane of the pupil provides a coherent hologram of the object's complex amplitude, from which a quantitative measure of its phase distribution can be extracted. The possibility of capturing simultaneously holograms of three-dimensional specimens, leading to three-dimensional reconstructions with absorption contrast, reflectance contrast, fluorescence contrast, as was previously demonstrated, and quantitative phase contrast, as shown here for the first time, opens up new avenues for multimodal imaging in biological studies.     

用于研究植物质外体空间三维结构的树脂铸型技术

本文介绍了用于研究植物体质外体空间三维结构的树脂铸型技术。植物包含许多重要的质外体空间,如木质部管状分子的腔隙、与气孔相连的叶肉细胞间的通气系统、分泌腔等等。这种空间的三维结构可借助于扫描电子显微镜(SEM)研究。但问题是,用SEM直接观察不到一个组织或细胞切面内部的图像,因此,不能观察它们的全貌。通过运用树脂铸型技术,可以获得完整的组织或腔隙内部空间的铸型。反映管壁结构的各种形象被印在铸型的表面上,在SEM下可对质外体空间进行详细研究。树脂铸型技术在结构植物学的研究上有重要的意义。     

Holographic interferometric measurement of motions in mature plants

Holographic interferometry has been used to plot graphs of the phototropic and geotropic bending undergone by a mature Stapelia variegata Linn over a 5-minute period. The holographic interferometric technique is shown to have the advantage of measuring displacements at least as small as 0.16 micrometers which permits observation of extremely slow plant motions over time periods of a few minutes. In addition, the holographic technique provides a permanent record of displacement information over the entire plant in a single hologram. The short 5-minute period required to produce a holographic interferogram has permitted the monitoring of slow plant motions by recording a series of consecutive holograms at 5-minute intervals over a 75-minute period. The results have been plotted on a graph thereby capturing for the first time such small displacement, velocity, and acceleration of a mature plant as a function of time.