Strategy for selection of methods for separation of bioparticles from particle mixtures

The desired product of bioprocesses is often produced in particulate form, either as an inclusion body (IB) or as a crystal. Particle harvesting is then a crucial and attractive form of product recovery. Because the liquid phase often contains other bioparticles, such as cell debris, whole cells, particulate biocatalysts or particulate by-products, the recovery of product particles is a complex process. In most cases, the particulate product is purified using selective solubilization or extraction. However, if selective particle recovery is possible, the already high purity of the particles makes this downstream process more favorable. This work gives an overview of typical bioparticle mixtures that are encountered in industrial biotechnology and the various driving forces that may be used for particle-particle separation, such as the centrifugal force, the magnetic force, the electric force, and forces related to interfaces. By coupling these driving forces to the resisting forces, the limitations of using these driving forces with respect to particle size are calculated. It shows that centrifugation is not a general solution for particle-particle separation in biotechnology because the particle sizes of product and contaminating particles are often very small, thus, causing their settling velocities to be too low for efficient separation by centrifugation. Examples of such separation problems are the recovery of IBs or virus-like particles (VLPs) from (microbial) cell debris. In these cases, separation processes that use electrical forces or fluid-fluid interfaces show to have a large potential for particle-particle separation. These methods are not yet commonly applied for large-scale particle-particle separation in biotechnology and more research is required on the separation techniques and on particle characterization to facilitate successful application of these methods in industry.     

Problem formulation and phenotypic characterisation for the development of novel crops

Phenotypic characterisation provides important information about novel crops that helps their developers to make technical and commercial decisions. Phenotypic characterisation comprises two activities. Product characterisation checks that the novel crop has the qualities of a viable product—the intended traits have been introduced and work as expected, and no unintended changes have been made that will adversely affect the performance of the final product. Risk assessment evaluates whether the intended and unintended changes are likely to harm human health or the environment. Product characterisation follows the principles of problem formulation, namely that the characteristics required in the final product are defined and criteria to decide whether the novel crop will have these properties are set. The hypothesis that the novel crop meets the criteria are tested during product development. If the hypothesis is corroborated, development continues, and if the hypothesis is falsified, the product is redesigned or its development is halted. Risk assessment should follow the same principles. Criteria that indicate the crop poses unacceptable risk should be set, and the hypothesis that the crop does not possess those properties should be tested. However, risk assessment, particularly when considering unintended changes introduced by new plant breeding methods such as gene editing, often ignores these principles. Instead, phenotypic characterisation seeks to catalogue all unintended changes by profiling methods and then proceeds to work out whether any of the changes are important. This paper argues that profiling is an inefficient and ineffective method of phenotypic characterisation for risk assessment. It discusses reasons why profiling is favoured and corrects some misconceptions about problem formulation.

     

Gonadotropin purification from horse serum applying magnetic beads

The glycoprotein hormone equine chorionic gonadotropin (eCG) is a commercial product used in animal breeding as well as in veterinary medicine. The current state of the art for the purification of eCG from serum is pH fractionation with metaphosphoric acid, two ethanol precipitation steps as well as dialysis followed by fixed-bed chromatography. Two simplified processes, including the use of magnetic microsorbents for the purification of eCG have been developed. The processes reduce or even omit the use of organic solvents and the required solid-liquid separation steps, thus making them potential candidates for a first commercial application of magnetic beads in bioprocessing.     

Agave as a biofuel feedstock in Australia

The opportunity for commercial production of Agave in Australia stems from the substantial carbohydrate and fibre content of Agave, the nature of carbohydrates stored, the pre‐existence of an Agave ethanol‐producing industry in Mexico, demand for biofuel feedstocks, impressive water‐use efficiencies of plants with the CAM pathway, and legislation mandating the ethanol content of fuel in Australia, where an estimated 748 ML will be required for blending with petrol by 2010–2011, compared with about 440 ML in 2009. Agave has potential as a crop for areas of seasonally limited rainfall in Australia, a judgement based upon desktop analyses and agronomic experience of growing Agave in Australia before 1915. Development of a viable Australian Agave farming system requires production be located in suitable regions, efficient propagation methods, mechanized production, and viable business plans at grower, processor and marketing levels. Growers and processors agree that Agave will not be grown commercially until plants are grown, maintained and harvested in Australia, product is produced and tested, and yield and risks are evaluated. To this end, Agave were imported into Australia from Mexico and a tissue culture propagation technique developed. A trial crop of Agave tequilana was planted in northern Queensland and CO₂ exchange, nitrogen and water dynamics, carbohydrate content, and system inputs and outputs are being monitored. The experience will be used to fine‐tune the farming system, assess production costs and develop robust life‐cycle assessments. Processing of plants from trials will test harvesting and transport infrastructure and will provide material to processors for testing. Samples will be provided to potential producers of value‐added products. An Australian Agave industry should provide opportunities for stimulating agronomic, scientific and commercial exchange between Australia and Mexico. Successful integration of Agave into Australian agriculture will require a biofuels‐focussed breeding programme in collaboration with Mexican researchers.     

Plant-made pharmaceuticals: leading products and production platforms

The number of approaches to recombinant protein production in plants is greater than ever before. Development of these new and improved technologies as production platforms for plant-made pharmaceuticals has and will continue to create new commercial opportunities in the pharmaceutical sector. However, it is inevitable that no single system will be optimal for the production of all recombinant proteins of interest in plants due to both the physical characteristics and the envisaged therapeutic application of each product. Here, we review a range of promising product/platform pairs emphasizing synergies during production and in clinical trials.     

Clinical application of breath biomarkers of oxidative stress status

Isolation and quantification of volatile breath biomarkers indicative of relevant alterations in clinical status has required development of new techniques and applications of existing analytical chemical methods. The most significant obstacles to successful application of this type of sample have been reduction in required sample volume permitting replicate analysis (an absolute requirement for all clinical studies), separation of the analyte(s) of interest from background molecules, water vapor and other molecules with similar physical properties, introduction of automation in analysis and the use of selective detection systems (electron impact mass spectrometry, flame photometric, thermionic detectors), and automated sample collection from the human subject. Advances in adsorption technology and trace gas analysis have permitted rapid progress in this area of clinical chemistry.     

Perfusion culture apparatus for suspended mammalian cells

A variety of processes have been proposed for mammalian cell culture in the commercial production of useful substances (e.g., monoclonal antibodies, therapeutic and diagnostics proteins). Among them, the perfusion culture of suspended non-immobilized cells is the most advantageous. Perfusion culture can be classified by the separation process of suspended cells from the culture mixture into three types, namely filtration, gravitational settling and centrifugation. From a commercial point of view, the present situation and technical problems of suspended-cell perfusion culture will be reviewed based on the three types, The recent development of perfusion culture has been carried out mainly on the filtration separation process, but the centrifugation process seems to have a promising future because of operation stability and scale-up feasibility. The reasons will be explained in details.     

The bioprocess–technological potential of the sea

Marine bioprocess engineers face a unique challenge for the millennium: designing methods for the sustainable development of known marine resources, as well as inventing a new generation of tools and processes that will enable a greater understanding of the ocean and its resources and lead to the discovery of new bioproducts for the future. The identification and application of novel, marine-derived pharmaceuticals, cosmetics, nutritional supplements, enzymes, and pigments have already been realized. The current and potential market value of these marine bioproducts is substantial. Continued discovery and development of marine resources will depend on a number of factors: identification of new bioproducts, sustainable use of the product, optimization of production, and efficient product recovery. Successfully addressing these challenges will require the integration and collaboration of mutidisciplinary teams of oceanographers, biologists, chemists, and engineers.     

Electrophoresis today and tomorrow: Helping biologists' dreams come true

Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two‐dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High‐throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser‐induced fluorescence detection of labeled DNA strands have been of key importance for the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH‐driven mobilization, provides efficient separations and on‐line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single‐cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single‐molecule detection.     

Discontinuous pH gradient-mediated separation of TiO2-enriched phosphopeptides

Global profiling of phosphoproteomes has proven to be a great challenge due to the relatively low stoichiometry of protein phosphorylation and poor ionization efficiency in mass spectrometers. Effective, physiologically relevant, phosphoproteome research relies on the efficient phosphopeptide enrichment from complex samples. Immobilized metal affinity chromatography and titanium dioxide chromatography can greatly assist selective phosphopeptide enrichment. However, the complexity of resultant enriched samples is often still high, suggesting that further separation of enriched phosphopeptides is required. We have developed a pH gradient elution technique for enhanced phosphopeptide identification in conjunction with titanium dioxide chromatography. Using this process, we demonstrated its superiority to the traditional “one-pot” strategies for differential protein identification. Our technique generated a highly specific separation of phosphopeptides by an applied pH gradient between 9.2 and 11.3. The most efficient elution range for high-resolution phosphopeptide separation was between pHs 9.2 and 9.4. High-resolution separation of multiply phosphorylated peptides was primarily achieved using elution ranges greater than pH 9.4. Investigation of phosphopeptide sequences identified in each pH fraction indicated that phosphopeptides with phosphorylated residues proximal to acidic residues, including glutamic acid, aspartic acid, and other phosphorylated residues, were preferentially eluted at higher pH values.     

Tools for Selective Enzyme Reaction Steps in the Synthesis of Laboratory Chemicals

The need for more selective reactions steps and the compatibility between process steps which follow on from each other has been a major driving force for organic synthesis. The synthesis of chiral compounds, metabolites, new chemical entities and natural products by a combination of chemical and enzyme reaction steps has become well established, due the existence of stable enzymes as selective catalysts which are inherently chiral by nature. Auxiliary tools such as suitable transfer reagents for reaching complete conversion, easy and robust reaction control as well as tools for straightforward workup and purification of the final product have been developed. Selective enzyme reaction steps in the area of hydrolyses, oxidation steps including hydroxylation and the Baeyer‐Villiger oxidation, carbon‐carbon bond formation and glycosylation reactions have compared favorably with existing methods of classical organic synthesis. The tools developed during optimization and scale‐up of these enzyme reaction steps have the potential to shorten development time. The introduction of selective enzyme reactions into an entire synthetic process has resulted in harmonization of improvements in economic efficiency with resultant solutions to health, safety and environment problems. This will become even more important in industrial synthetic chemistry in the future, for convenient solutions to certain intractable synthetic problems and for expanding the repertoire of chemistry by modular biocatalysts. Efficient isolation procedures for the final product are essential to take full advantage of the biocatalytic conversion to obtain high product yields.     

Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome: optimization and protein database

In biomarker discovery, the detection of proteins with low abundance in the serum proteome can be achieved by optimization of protein separation methods as well as selective depletion of the higher abundance proteins such as immunoglobins (e.g. IgG) and albumin. A relative newcomer to the proteomic separation arena is the commercial instrument PF2D from Beckman Coulter that separates proteins in the first dimension using chromatofocusing followed in line by reversed phase chromatography in the second dimension, thereby separating intact proteins based on pI and hydrophobicity. In this study, assessment and optimization of serum separation (undepleted serum and albumin-IgG-depleted serum) by the PF2D is presented. Protein databases were created for serum obtained from a healthy individual under traditional and optimized methods and under different sample preparation protocols. Separation of the doubly depleted serum using the PF2D with 20% isopropanol present in the first dimension running buffer allowed us to unambiguously identify 150 non-redundant serum proteins (excluding all immunoglobulin and albumin, a minimum of two peptide matches with acceptable Mascot score) in which 81 have not been identified previously in serum. Among them, numerous cellular proteins were identified to be specifically the skeletal muscle isoform, such as skeletal muscle fast twitch isoforms of troponin T, myosin alkali light chain 1, and sarcoplasmic/endoplasmic reticulum calcium ATPase. The detection of specific skeletal muscle protein isoforms in the serum from healthy individuals reflects the physiological turnover that occurs in skeletal muscle, which will have an impact on the ability to use generic "cellular" proteins as biomarkers without further characterization of the precise isoforms or post-translational modifications present.     

Towards tailor-made oligosaccharides—chemo-enzymatic approaches by enzyme and substrate engineering

Carbohydrate structures have been identified in eukaryotic and prokaryotic cells as glycoconjugates with communication skills. Their recently discussed role in various diseases has attracted high attention in the development of simple and convenient methods for oligosaccharide synthesis. In this review, recent approaches combining nature’s power for the design of tailor made biocatalysts by enzyme engineering and substrate engineering will be presented. These strategies lead to highly efficient and selective glycosylation reactions. The introduced concept shall be a first step in the direction to a glycosylation toolbox which paves the way for the tailor-made synthesis of designed carbohydrate structures.     

Validation procedures of sedimentation field-flow fractionation techniques for biological applications

Sedimentation field-flow fractionation (SdFFF) offers great potential for the separation of submicrometer and micrometer-sized species. The availability of commercial instrumentation and the versatility of this method originated its success. At this stage of development, SdFFF techniques are mature enough for use in analytical research, development and even routine work. However, prior to their use, these techniques like any other methodologies, have to be validated. As the application of SdFFF techniques to cell separation is being constantly developed, we have investigated separation performance according to validation rules classically defined for separation methods (chromatography) in the case of cellular materials.     

An improved pulsed-field polyacrylamide gel electrophoresis system for physical selection of linking clones: isolation of SfiI linking clones from a chromosome 21-specific library

We had previously developed an efficient procedure for selective cloning of rare-cutter linking fragments that is based on physical separation of linking clone DNAs by pulsed-field polyacrylamide gel electrophoresis (PF-PAGE). An advantage of the physical selection procedure over the conventional cloning-based ones utilizing the insertion of selection marker or vector sequences into the rare-cutter sites is that it can be readily applied to the selection of linking fragments for rare-cutters, generating ambiguous cohesive end sequences such as SfiI (GGCCNNNN/NGGCC). In the present work, the physical separation procedure was improved by introducing a discontinuous buffer system into PF-PAGE, and its feasibility was exemplified by the selective isolation of SfiI linking clones from a human chromosome 21-specific library. This simple and efficient procedure will provide a useful tool for genome analysis.     

Bioseparation and bioanalytical techniques in environmental monitoring

The growing use of antibody-based separation methods has paralleled the expansion of immunochemical detection methods in moving beyond the clinical diagnostic field to applications in environmental monitoring. In recent years high-performance immunoaffinity chromatography, which began as a separation technique in biochemical and clinical research, has been adapted for separating and quantifying environmental pollutants. Bioaffinity offers a selective biological basis for separation that can be incorporated into a modular analytical process for more efficient environmental analysis. The use of immunoaffinity chromatography for separation complements the use of immunoassay for detection. A widely used immunochemical detection method for environmental analyses is enzyme immunoassay. The objective of this paper is to review the status of bioaffinity-based analytical procedures for environmental applications and human exposure assessment studies. Environmental methods based on bioaffinity range from mature immunoassays to emerging techniques such as immunosensors and immunoaffinity chromatography procedures for small molecules.     

Screening for soluble expression of recombinant proteins in a 96-well format

For future structural and functional genomics programs new tools will be required. The implementation of high-throughput (HTP) methods for protein production will be an essential element. Present HTP protein production developments in structural genomics are aimed at obtaining well-expressing and highly soluble proteins, which are preferred candidates for structure-function studies. Here, we describe a cheap and efficient procedure to identify well-expressing soluble proteins in Escherichia coli in a compact 96-well format. Reproducible lysis on filter plates, followed by a filtration step on 96-well filter plates, allows the efficient separation of inclusion bodies from the soluble fraction. In the following step a dot blot procedure using anti-RGS-His(4) antibody (Qiagen) to detect expression of recombinant His-tagged protein is applied allowing direct detection of the target protein in the soluble fraction. The method is well suited for automation and should be applicable to expression screening of most proteins and fusion domains to which specific antibodies are available.     

Localization properties of fluorescence cytochemical enzyme procedures

Fluorescence enzyme cytochemical procedures will contribute significantly to biomedical problems where knowledge of the enzymic composition of individual cells is important. Compared with the number of absorbance enzyme cytochemical methods, relatively few fluorescence procedures have been reported. In this paper, the merits of the described methods are discussed. A distinction is made between methods with and without a capture reaction. Only a few methods satisfy the requirement of accurate localization of the final product and high signal to noise ratios. Thus, there still is a need for valid fluorescence cytochemical enzyme methods. It is concluded that the bottle neck for valid fluorescence cytochemical enzyme methods is the development of efficient fluorogenic capture reactions for the primary enzyme products.     

Removal of cesium ions from aqueous solutions using various separation technologies

Cesium is the major fission product of uranium, which widely exists in radioactive wastewater. Radiocesium has potential adverse effects on human health and ecological environment. Different methods such as chemical precipitation, coagulation/co-precipitation, solvent extraction, membrane process, chemical reduction, and adsorption have been used to remove radioactive cesium from aqueous solution. However, the development of innovative technologies capable of selectively removing radioactive cesium is still imperative yet challenging. This review focused on cesium removal using various separation technologies, including chemical precipitation, solvent extraction, membrane separation, and adsorption. The key restraints for cesium removal, as well as the recent progress of these methods have also been discussed. Particular attention has been paid to the adsorption methods, which has been highlighted by introducing the latest advances in inorganic adsorbents (such as metal hexacyanoferrates, clay minerals, carbon-based-adsorbents, and ammonium molybdophosphate), organic adsorbents (such as ion exchange resin, metal–organic frameworks and supramolecular/indicator grafting adsorbents), and biosorbents (such as agroforestry wastes and microbial biomass). Adsorption-based methods are high efficient in separation of cesium ions from aqueous streams, and adsorption of cesium ions has been investigated intensively and even used in practical applications, there is still considerable scope for improvement in terms of adsorption capacity and selectivity.

     

Acetic anhydride requirement in the colorimetric determination of tryptophan

Nucleic acid research frequently necessitates the analytical resolution of nucleic acid derivatives. Thin-layer chromatography (tlc), for its simplicity, short development time, and superior resolving power, is often preferable to other methods (1–3). Although the literature contains a large number of methods that have been devised for the separation of purine and pyrimidine derivatives (4,5) no tlc technique has hitherto been described for the concomitant separation of bases, nucleosides, nucleoside 5′-monophosphates, nucleoside 3′-monophosphates, nucleoside diphosphates, and nucleoside triphosphates.The present communication deals with methods devised for the simultaneous separation of the above-mentioned pyrimidine derivatives. They enable the resolution of either the six uracil derivatives or the six cytosine derivatives, on commercial cellulose tlc sheets. Alternatively, the six pyrimidine derivatives can be separated on cellulose layers 0.75 mm thick. Since formic acid extracts of bacterial cells do not interfere with the separation, these methods can be used for the direct estimation of extracts of biological materials.