Enzyme catalysed reactions in water - Organic solvent two-phase systems

Enzyme-catalysed transformations carried out in two-phase systems consisting of water and a water-immiscible organic solvent are discussed. The systems appear advantageous when substrates poorly soluble in water, such as steroids, are used. The methodology also makes possible the use of hydrolytic enzymes for the synthesis of ester bonds. Several applications of such two-phase systems are illustrated. The criteria that must be taken into consideration for selecting the most suitable organic solvents and the operational conditions are discussed.     

Evidence for Inhibitory Allelopathic Interactions Involving Phenolic Acids in Field Soils: Concepts vs. an Experimental Model

The accepted criteria for identifying allelopathic interactions in the field that have been proposed in the literature offer heuristic function, but to date have failed as a framework for research and diagnostics. If the present criteria are to be modified to make them useful empirically, their shortcomings must be identified. For this review, data from the literature and from defined model systems consisting of plants, soil, and/or microbes are used to evaluate the applicability of the accepted criteria to defined systems in which plants are responding to known allelochemicals. Based on this evaluation, modified criteria are proposed. In many respects, however, the modified criteria are as difficult to satisfy in the field as those proposed previously. The new criteria have value as a research framework because they clearly suggest that a shift in research focus to the soil environment, specifically the barrier of the rhizosphere through which allelochemicals must pass, is essential if the role of allelopathic interactions in the field is to be established.     

Non-leaky vesiculation of large unilamellar vesicles (LUV) induced by plasma high density lipoproteins (HDL): detection by HPLC

Interaction of large unilamellar phosphatidylcholine vesicles (LUV, 75nm) and plasma high density lipoproteins (HDL) resulted in a non-leaky vesiculation of LUV. This vesiculation was detected by a HPLC-system consisting of a combination of three TSK-gel columns (6000PW, 5000PW, 3000SW). With increasing incubation time liposomal [14C]PC, entrapped [3H]inulin, and apoprotein of HDL origin decreased. The decrease was accompanied by a formation of new particles, consisting of liposomal PC and apoprotein. These particles also enclosed [3H]inulin, reflecting a hydrophilic inner space. The formation of the particles reached a maximum after one day of incubation. Retention time was 21 minutes for LUV, 28 minutes for the new particles, and 36 minutes for HDL. In vesicles with membranes consisting of phosphatidylcholine and 30% cholesterol no interactions were observed.     

Cover Picture: Biotechnology Journal 6/2010

Cover illustration: Biotech Methods and Advances. This issue of Biotechnology Journal covers methods for systems metabolic engineering as well as downstream processing. The cover image shows an artist's impression of a magnetic fusion protein consisting of antibody like particles (pale blue) and ferritin subunits (pale green) encapsulating an iron core (red). These “Magnetizable antibody-like proteins” are described by Dehal et al. pp. 596–605 (http://dx.doi.org/10.1002/biot.200900273). Art by Mark Bradshaw, Pixelweave 3D.     

Effect of MOI ratio on the composition and yield of chimeric infectious bursal disease virus-like particles by baculovirus co-infection: deterministic predictions and experimental results

Virus-like particles (VLPs) are empty particles consisting of virus capsid proteins that closely resemble native virus but are devoid of the native viral nucleic acids and therefore have attracted significant attention as noninfectious vaccines. A recombinant baculovirus, vIBD-7, which encodes the structural proteins (VP2, VP3, and VP4) of infectious bursal disease virus (IBDV), produces native IBD VLPs in infected Spodoptera frugiperda insect cells. Another baculovirus, vEDLH-22, encodes VP2 that is fused with a histidine affinity-tag (VP2H) at the C-terminus. By co-infection with these two baculoviruses, hybrid VLPs with histidine tags were formed and purified by immobilized metal affinity chromatography (Hu et al., 1999). Also, we demonstrated that varying the MOI ratio of these infecting viruses altered the extent of VP2H incorporated into the particles. A dynamic mathematical model that described baculovirus infection and VLP synthesis (Hu and Bentley, 2000) was adapted here for co-infection and validated by immunofluorescence labeling. It was shown to predict the VLP composition as a dynamic function of MOI. A constraint in the VP2H content incorporated into the particles was predicted and shown by experiments. Also, the MOI ratio of both infecting viruses was shown to be the major factor influencing the composition of the hybrid particles and an important factor in determining the overall yield. ELISA results confirmed that VP2H was exhibited to a varied extent on the outer surface of the particles. This model provides insight on the use of virus co-infection in virus-mediated recombinant protein expression systems and aids in the optimization of chimeric VLP synthesis.     

STUDY OF MITOCHONDRIA IN RAT LIVER : Quantitative Electron Microscopy

The electron microscope has been used to determine the weight distribution of isolated subcellular particles from normal rat liver. The following results are reported: (1) There exist at least two well defined weight populations of subcellular particles; their respective median weights are 1.3 x 10^-14 and 11 x 10^-14 gm. The lighter fraction is considered to consist of lysosomes, the heavier of mitochondria. (2) The mitochondrial fraction shows a log-normal distribution of the particle weight. (3) By the introduction of morphologic criteria, the mitochondrial fraction is divided into two groups, one consisting of a spherical, the other of an oblong type of particle. The data found support the following concepts: (a) Mitochondria increase their weight from a certain size up by linear growth. (b) Mitochondria divide. The division is not necessarily symmetric; in all cases, however, one part of the division product is a spherical particle. It is felt that these results constitute a valuable demonstration of the general capabilities of quantitative electron microscopy and may stimulate many other useful applications of this technique in cytology, bacteriology, and virology.     

Affinity-specific protein separations using ligand-coupled particles in aqueous two-phase systems: II. Recovery and purification of pyruvate kinase and alcohol dehydrogenase from Saccharomyces cerevisiae

The novel approach of using aqueous two-phase systems for the elution of protein from ligand-coupled particles is investigated using pyruvate kinase and alcohol dehydrogenase from recombinant Saccharomyces cerevisiae and Cibacron blue F3G-A-coupled Sepharose CL6B (Blue-Sepharose) particles as a model system. The ligand-coupled particles distribute quantitatively to the polyethylene glycol-(PEG-) rich top phase and the recovered enzymes partition selectively to the dextran-(DEX-) rich bottom phase. An effective recovery and partial purification of pyruvate kinase and alcohol dehydrogenase from Blue-Sepharose particles using PEG8000-DEXT500 aqueous two-phase systems are demonstrated through a modest increase of salt concentration. The bioselective eluting agent, MgADP, which is useful in chromatographic operations, is not required for the process using aqueous two-phase systems. Recovery of pyruvate kinase, which is bound to ligand-coupled particles, in the DEX-rich bottom phase of aqueous two-phase systems can be up to 95% in one-step operations. The mixing time of ligand-coupled particles with aqueous two-phase systems is a major controlling variable. The salt concentration, the molecular weight of polymer, and the total volume of aqueous two-phase systems also influence the recovery of pyruvate kinase from ligand-coupled particles. The recovered enzymes in the DEX-rich bottom phase remain biologically stable over a long period of storage time. The concentration of product protein in a reduced volume and the easy separation from ligand-coupled particles are added advantages of the process using aqueous two-phase systems. Preliminary studies with goat polyclonal anti-pyruvate kinase-coupled Sepharose particles indicate that the process also may be applicable when a high-affinity ligand such as antibody is used. The experimental results and a theoretical derivation based on equilibrium models for binding/dissociation of ligands and proteins show that the process results in better recovery as compared to that of conventional bulk elution techniques.     

Magnetizable antibody-like proteins

Use of paramagnetic particles to isolate molecules or cells from complex media is well established. Typically, particles are manufactured and coated with a biological molecule that confers specific biorecognition. Incubation of particles with sample and exposure to magnetic fields isolates the species of interest. We have designed, produced and assessed magnetized fusion proteins consisting of the antigen-binding portion of an antibody (single chain variable fraction; scFv) fused to the heavy chain of the iron-binding protein ferritin. The fusion protein subunits expressed in E. coli assemble to form a fusion protein consisting of a ferritin sphere with scFvs on the surface. The fusion proteins were chemically magnetized by introducing a paramagnetic iron core. The resultant fusion protein was shown to be magnetizable and capable of binding target antigens. These “organic” magnetizable particles possess a number of theoretical advantages over traditional inorganic particles.     

Mathematical Model for Low Density Lipoprotein (LDL) Endocytosis by Hepatocytes

Individuals with elevated levels of plasma low density lipoprotein (LDL) cholesterol (LDL-C) are considered to be at risk of developing coronary heart disease. LDL particles are removed from the blood by a process known as receptor-mediated endocytosis, which occurs mainly in the liver. A series of classical experiments delineated the major steps in the endocytotic process; apolipoprotein B-100 present on LDL particles binds to a specific receptor (LDL receptor, LDL-R) in specialized areas of the cell surface called clathrin-coated pits. The pit comprising the LDL–LDL-R complex is internalized forming a cytoplasmic endosome. Fusion of the endosome with a lysosome leads to degradation of the LDL into its constituent parts (that is, cholesterol, fatty acids, and amino acids), which are released for reuse by the cell, or are excreted. In this paper, we formulate a mathematical model of LDL endocytosis, consisting of a system of ordinary differential equations. We validate our model against existing in vitro experimental data, and we use it to explore differences in system behavior when a single bolus of extracellular LDL is supplied to cells, compared to when a continuous supply of LDL particles is available. Whereas the former situation is common to in vitro experimental systems, the latter better reflects the in vivo situation. We use asymptotic analysis and numerical simulations to study the longtime behavior of model solutions. The implications of model-derived insights for experimental design are discussed.     

Soil-derived organic particles and their effects on the community of culturable microorganisms

Soil microbial community interacts with a range of particulate material in the soil, consisting of both inorganic and organic compounds with different levels of water solubility. Though sparingly water-soluble and insoluble organic compounds in the soil may affect living organisms, they are difficult to introduce into microbiological media. Their biological activity (i.e., their effect on soil microorganisms) thus has been almost neglected in most of the cultivation assays. To fill this gap, we propose the use of fine organic particles prepared from soil organic matter that are introduced into a laboratory medium where microbial community is cultivated. To this purpose, submicrometer particles consisting of sparingly water-soluble or insoluble soil organic matter were obtained from humic horizons of two soils by precipitation of organics dissolved in tetrahydrofuran by addition of water. The particles could then be size fractionated by centrifugation, and coarse fraction obtained from humic horizon formed under spruce forest was tested for effects on complex microbial community developing under laboratory conditions. The results indicate that low concentration (20 mg/L) of the particles is efficient to affect the composition of the bacterial community revealed by terminal restriction fragment length polymorphism. The work contributes to understanding the factors that determine the composition of soil microbial community.     

Multiple correlative immunolabeling for light and electron microscopy using fluorophores and colloidal metal particles.

Multiple correlative immunolabeling permits colocalization of molecular species for sequential observation of the same sample in light microscopy (LM) and electron microscopy (EM). This technique allows rapid evaluation of labeling via LM, prior to subsequent time-consuming preparation and observation with transmission electric microscopy (TEM). The procedure also yields two different complementary data sets. In LM, different fluorophores are distinguished by their respective excitation and emission wavelengths. In EM, colloidal metal nanoparticles of different elemental composition can be differentiated and mapped by energy-filtering transmission electron microscopy with electron spectroscopic imaging. For the highest level of spatial resolution in TEM, colloidal metal particles were conjugated directly to primary antibodies. For LM, fluorophores were conjugated to secondary antibodies, which did not affect the spatial resolution attainable by fluorescence microscopy but placed the fluorophore at a sufficient distance from the metal particle to limit quenching of the fluorescence signal. It also effectively kept the fluorophore at a sufficient distance from the colloidal metal particles, which resulted in limiting quenching of the fluorescent signal. Two well-defined model systems consisting of myosin and alpha-actinin bands of skeletal muscle tissue and also actin and alpha-actinin of human platelets in ultrathin Epon sections were labeled using both fluorophores (Cy2 and Cy3) as markers for LM and equally sized colloidal gold (cAu) and colloidal palladium (cPd) particles as reporters for TEM. Each sample was labeled by a mixture of conjugates or labels and observed by LM, then further processed for TEM.     

HIV-1壳体蛋白的结构及其病毒样颗粒疫苗

人类免疫缺陷病毒(HIV)的壳体蛋白(CA)在HIV病毒的组装和成熟过程中起着至关重要的作用。近年来,壳体蛋白的体外表达及其疫苗的研制成了HIV各项研究的焦点。由于壳体蛋白具有较好的的保守性,用其制得的疫苗也会提供比包膜蛋白更为广泛的免疫保护力。另外若将CA在体外表达成一个颗粒状结构,会增强其免疫原性,可以使疫苗发挥出更大的效力。     

Distribution of sodium-plus-potassium-stimulated adenosine-triphosphatase activity in isolated nerve-ending particles

1. A rapid method for the isolation of nerve-ending particles from brain is described. This involved the centrifugation of the large-granule fraction over a discontinuous density gradient consisting of 3% (w/v) and 13% (w/v) Ficoll dissolved in 0.32m-sucrose. The results of the biochemical as well as morphological identification of nerve-ending particles are given. 2. Approx. 20% of the (Na(+)+K(+))-stimulated adenosine-triphosphatase activity originally present in the cerebral grey-matter suspension was recovered in the fraction consisting principally of large nerve-ending particles (approx. 1mu in diameter). The activity of the adenosine triphosphatase/mg. of protein in the nerve-ending fraction approximated to that in the small-granule fraction after the treatment with glycol ether diamine-tetra-acetic acid. The conclusion was drawn that the synaptic structure, supposedly the limiting membrane of the nerve-ending particle, is one of the feasible sites of localization of the (Na(+)+K(+))-stimulated adenosine-triphosphatase activity in cerebral tissues. Adenosine triphosphatase in purified cerebral mitochondria was not stimulated by Na(+). 3. No qualitative differences were found between the (Na(+)+K(+))-stimulated adenosine-triphosphatase activities exhibited by the nerve-ending particles and by the cerebral small-granule fraction with respect to pH-dependence, cation requirements and susceptibility to ouabain.     

Application of real-time radiation dosimetry using a new silicon LET sensor

A new type of real-time radiation monitoring device, RRMD-III, consisting of three double-sided silicon strip detectors (DSSDs), has been developed and tested on-board the Space Shuttle mission STS-84. The test succeeded in measuring the linear energy transfer (LET) distribution over the range of 0.2 keV/micrometer to 600 keV/micrometer for 178 h. The Shuttle cruised at an altitude of 300 to 400 km and an inclination angle of 51.6 degrees for 221.3 h, which is equivalent to the International Space Station orbit. The LET distribution obtained for particles was investigated by separating it into galactic cosmic ray (GCR) particles and trapped particles in the South Atlantic Anomaly (SAA) region. The result shows that the contribution in dose-equivalent due to GCR particles is almost equal to that from trapped particles. The total absorbed dose rate during the mission was 0.611 mGy/day; the effective quality factor, 1.64; and the dose equivalent rate, 0.998 mSv/day. The average absorbed dose rates are 0.158 mGy/min for GCR particles and 3.67 mGy/min for trapped particles. The effective quality factors are 2.48 for GCR particles and 1.19 for trapped particles. The absorbed doses obtained by the RRMD-III and a conventional method using TLD (Mg(2)SiO(4)), which was placed around the RRMD-III were compared. It was found that the TLDs showed a lower efficiency, just 58% of absorbed dose registered by the RRMD-III.     

Biochemical study of KB-cell receptor for adenovirus

Three different approaches were used in an attempt to characterize the KB-cell receptor for adenovirus: affinity chromatography, immunoadsorption and cross-linking with a cleavable bifunctional reagent. The first system used an affinity gel consisting of adenovirus-fibre projection linked to Sepharose matrix by an intermediate bis(aminopropyl)amine arm, the amino groups of the fibre ligand being preserved by prior citraconylation. The second system consisted of adenovirus complete penton capsomere attached to anti-(penton base) antibody and cross-linked to polyacrylamide particles with glutaraldehyde. In this latter affinity model, the penton-fibre projection was appropriately oriented outwards, as in the virus particle. Both affinity systems permitted isolation from a KB-cell plasma-membrane extract of fibre-binding and penton-fibre-binding protein material, which inhibited adenovirus attachment. The penton-immunoadsorbent appeared more efficient and more specific than the affinity column of fibre-bis(aminopropyl)amino-Sepharose gel in specific activity of inhibition of adenovirus attachment. The third method consisted of reversibly cross-linking KB-cell receptor proteins with adenovirus particles by means of a cleavable di-imidoester and isolation of the complexes by sucrose-density-gradient centrifugation. Polypeptide analysis on sodium dodecyl sulphate/polyacrylamide gel of labelled KB-cell surface proteins, selected by the different procedures, showed that three major protein subunits of 78000, 42000 and 34000mol.wt. were common to the three selection systems. A possible model for the structure and function of the KB-cell receptor for adenovirus is discussed.     

A dynamic mathematical model for microbial removal of pyritic sulfur from coal

A dynamic mathematical model has been developed to describe microbial desulfurization of coal by Thiobacillus ferrooxidans. The model considers adsorption and desorption of cells on coal particles and microbial oxidation of pyritic sulfur on particle surfaces. The influence of certain parameters, such as microbial growth rate constants, adsorption-descrption constants, pulp density, coal particle size, initial cell and solid phase substrate concentration on the maximum rate of pyritic sulfur removal, have been elucidated. The maximum rate of pyritic sulfur removal was strongly dependent upon the number of attached cells per coal particle. At sufficiently high initial cell concentrations, the surfaces of coal particles are nearly saturated by the cells and the maximum leaching rate is limited either by total external surface area of coal particles or by the concentration of pyritic sulfur in the coal phase. The maximum volumetric rate of pyritic sulfur removal (mg S/h cm(3) mixture) increases with the pulp density of coal and reaches a saturation level at high pulp densities (e.g. 45%). The maximum rate also increases with decreasing particle diameter in a hyperbolic form. Increases in adsorption coefficient or decreases in the desorption coefficient also result in considerable improvements in this rate. The model can be applied to other systems consisting of suspended solid substrate particles in liquid medium with microbial oxidation occurring on the particle surfaces (e.g., bacterial ore leaching). The results obtained from this model are in good agreement with published experimental data on microbial desulfurization of coal and bacterial ore leaching.     

Bridging structures spanning the junctioning gap at the triad of skeletal muscle

The membrane systems of skeletal muscle were examined after tannic acid fixation. A new structure consisting of bridges spanning the junctional gap is described, and a model is proposed in which the cytoplasmic but not the luminal membrane leaflets of the transverse tubule and of the junctional sarcoplasmic reticulum (SR) are continuous. The globular particles (presumably the Ca-binding proteins) within the terminal cisternae were arranged in longitudinal rows and appeared adherent to the junctional membrane. The junctional gap was present in negatively stained, frozen thin sections of fixed muscles. Negatively staining material occured within the junctional gap. The cytoplasmic leaflets of the longitudinal, intermediate, and terminal cisterna regions of the SR exhibited a thick coat of densely staining material compatible with the presence of the Ca-ATPase. Similar bridges were also observed at the surface membrane-SR close coupling sites of vascular smooth muscle.     

Synthesis in yeast of hepatitis B virus surface antigen modified P31 particles by gene modification

The pre-S2 portion of hepatitis B virus surface antigen P31 gene was modified to make gene products resistant to trypsin-like proteases in Saccharomyces cerevisiae. The coding sequence for 6 amino acids (Ser44 - Thr49) including Arg48 was removed, and the altered gene was inserted into an expression vector. The modified HBsAg P31 (M-P31c) gene products, consisting of GP37 and GP34, formed particles having both HBsAg antigenicity and polymerized-albumin receptor activity. Since the M-P31c particles can elicite two kinds of protective antibodies against hepatitis B virus, anti-S and anti-pre-S2 antibodies, the M-P31c particles are expected to be potentially effective to S-nonresponders.     

On the Stereological Estimation of Numerical Density of Particle Systems by an Object Counting Method

The determination of numerical density Nv of particles is one of the most complex problems in stereology. This paper presents a method for solving it, consisting only of counting of intersections between particles and thick slices of some different thicknesses. The essential stereological parameters Nv and mean caliper diameter D of the particles are determined by means of a regression line. The basic formula is a simple consequence of general principles for deriving stereological formulae which is described in this paper. The object counting method is applicable if the particles are convex and if the whole particle system can be described by a stationary isotropic ergodic marked point process. A practical example (liver cell nuclei of rats) demonstrates the application of the method.     

Modeling and measuring urban sustainability in multi-criteria based systems — A challenging issue

This paper addresses how urban sustainability is modeled and the ways criteria-based systems deal with its measurability for an effective and reliable assessment. Twelve sustainability models are reviewed and a subset is briefly presented. More importantly, this research work investigates five national rating systems of sustainable urban development compared with the newly developed CAMSUD system. The comparison focuses on the systems' structure, categorization, technical content and measurability. The main findings about the selected national rating systems thoroughly discussed in the paper are: (i) They all have a tree-like structure, (ii) their conceptualization and categorization follow three or four sustainability pillars models, sustainability topics or spatial scale; (iii) they use either planning-oriented or performance-oriented weighting approaches; (iv) the criteria are defined as sustainability goals, action measures or assignments to be fulfilled; (v) the sustainability items can hardly be juxtaposed since they are differently handled, (vi) overlapping criteria might occur, (vii) similar criteria can be categorized under different categories and this affects the emphasis put on these categories, (viii) all criteria are independently rated with no consideration of mutual interrelationships. In an attempt to solve some of these weaknesses, the newly developed CAMSUD system is introduced as alternative and relies on the following: (i) the system structure is considered as a network, (ii) the conceptualization and categorization is based on spatial scaling as well as on sustainability topics and pillars, (iii) many criteria are directly planning-relevant (23 of 40), (iv) the criteria are defined as sustainability goals rather than action measures and (v) the quantification of criteria is planned as to account for mutual interactions.