A method for three-dimensional protein characterization and its application to a complex plant (corn) extract

Knowledge of host protein properties is critical for developing purification methods for recombinant proteins from a specific host, or for choosing suitable hosts and targeted expression tissues for a specific recombinant protein. A method to obtain a three-dimensional (3D) map (surface hydrophobicity (SH), isoelectric point (pI), and molecular weight (MW)), of a host's aqueous soluble protein properties was developed. The method consists of hydrophobic partitioning in a PEG 3350 (15.7%)-Na(2)SO(4) (8.9%)-NaCl (3%) aqueous two-phase (ATP) system followed by quantitative, 2D-electrophoretic characterization of the proteins of each equilibrium phase and the original extract. The pI and MW of host proteins were obtained directly through 2D electrophoresis. The partition coefficients of individual proteins were obtained by quantitative matching of protein spots in the top and bottom phase gels and calculating the protein partition coefficients from this information. Correlation of the partition coefficient to a SH scale was established by partitioning several model proteins with known surface hydrophobicities in the same ATP system. The inclusion of the extract gel provided for a spot selection criterion based on satisfactory mass balance closure. The method is illustrated by application to a mixture of model proteins and to complex mixtures, that is, corn germ proteins extracted at pH 7 and pH 4.     

Aqueous biphasic systems composed of ionic liquids and sodium carbonate as enhanced routes for the extraction of tetracycline

Aqueous biphasic systems (ABS) using ionic liquids (ILs) offer an alternative approach for the extraction, recovery, and purification of biomolecules through their partitioning between two aqueous liquid phases. In this work, the ability of a wide range of ILs to form ABS with aqueous solutions of Na₂CO₃ was evaluated. The ABS formed by IL + water + Na₂CO₃ were determined at 25°C, and the respective solubility curves, tie‐lines, and tie‐line lengths are reported. The studied ILs share the common chloride anion, allowing the IL cation core, the cation isomerism, the presence of functionalized groups, and alkyl side chain length effects to be evaluated. An increase in the cation side alkyl chain length leads to a higher ability for liquid–liquid demixing whereas different positional isomers and the presence of an allyl group have no major influence in the phase diagrams behavior. Quaternary phosphonium‐ and ammonium‐based fluids are more able to form an ABS when compared with imidazolium‐, pyridinium‐, pyrrolidinium‐, and piperidium‐based ILs. Moreover, the presence of an aromatic cation core has no major contribution to the formation of ABS when compared to the respective nonaromatic counterparts. Finally, to appraise on the systems applicability in downstream processing, selected systems were used for the partitioning of tetracyclines (neutral and salt forms) — a class of antibiotics produced by bacteria fermentation. Single‐step extraction efficiencies for the IL‐rich phase were always higher than 99% and confirm the great potential of ILs to be applied in the biotechnological field. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:645–654, 2013     

Different types of aqueous two‐phase systems for biomolecule and bioparticle extraction and purification

Upstream improvements have led to significant advances in the productivity of biomolecules and bioparticles. Today, downstream processes are the bottleneck in the production of some biopharmaceuticals, a change from previous years. Current purification platforms will reach their physical limits at some point, indicating the need for new approaches. This article reviews an alternative method to extract and purify biomolecules/bioparticles named aqueous two‐phase system (ATPS). Biocompatibility and readiness to scale up are some of the ATPS characteristics. We also discuss some of ATPS applications in the biotechnology field. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1343–1353, 2013     

A rapid method for measuring organelle-specific substrate transport in homogenates from plant tissues

A rapid method is described for measuring organelle-specific metabolite transport systems in crude homogenates from plants. The tissues were homogenized in liquid nitrogen, extracted with buffer and reconstituted into artificial membranes. The method allowed demonstration of the known different substrate specificities of chloroplast triose phosphate/phosphate translocators from C₃- and C₄-plants, of the triose phosphate/phosphate translocator from non-green tissue, and of the dicarboxylate translocator. It thus by-passes the necessity to isolate intact plant organelles and, in addition, only a low amount of tissue material is required for transport measurements.Abbreviations Chl chlorophyll - TPT triose phosphate/phosphate translocator Dedicated to Professor F.-C. Czygan on the occasion of his 60th birthdayThis research was supported by the Bundesministerium für Forschung und Technologie. A.W. is a recipient of a Ph.D. fellowship from the Deutsche Forschungsgemeinschaft.     

A bioassay for insect deterrent compounds found in plant and animal tissues

A general field bioassay for detecting biologically active compounds in plants and insects has been developed and tested for efficacy and sensitivity. Methanolic extracts, in sucrose solution, of 20 plant and six caterpillar species were offered to the ponerine ant Paraponera clavata and the feeding preferences observed. The bioassay resulted in the detection of nine plant and three caterpillar species with ant-deterrent extracts, and 11 plant and three caterpillar species with neutral or attractant extracts. All of the plants showing ant-deterrent characteristics which had been chemically investigated in our laboratory, or for which chemical literature was available, contained secondary metabolites of known deterrence. Both naturally occurring and artificial differences in chemical concentrations could be detected using the bioassay. The method provides a means of screening plants and insects for compounds that are insect anti-feedants or that can modify insect behaviour.     

Reactions of alpha amylases with starch granules in aqueous suspension giving products in solution and in a minimum amount of water giving products inside the granule

Porcine pancreatic alpha amylase (PPA) and Bacillus amyloliquefaciens alpha amylase (BAA) were allowed to react with starch granules from maize, waxy maize, amylomaize-7, and potato in an aqueous suspension with a starch to water ratio of 1:10 and in a minimum of water with a starch to water ratio of 1:1. Quantitative amounts of the maltodextrin products were determined by TLC and scanning densitometry. The two alpha amylases gave different products that were characteristic of their unique action patterns. The percent conversion differed for the different kinds of starches and for the two kinds of reaction conditions. Maize and waxy maize starches were converted into about twice as much maltodextrins than were amylomaize-7 and potato starches by both enzymes and under both reaction conditions. The aqueous suspension gave much greater conversion into maltodextrins than did the minimum water condition. BAA gave 3-14% greater conversion of the granules into maltodextrins than did PPA, with the exception of potato starch.     

A sensitive method for confocal fluorescence microscopic visualization of starch granules in iodine stained samples

Synthesized by glycogen synthase and starch synthases (SS) using ADP-glucose as the sugar donor molecule, glycogen and starch accumulate as predominant storage carbohydrates in most bacteria and plants, respectively. We have recently shown that the so-called “starch-less” Arabidopsis thaliana adg1–1 and aps1 mutants impaired in ADP-glucose pyrophosphorylase do indeed accumulate low starch content in normal growth conditions, and relatively high starch content when plants were cultured in the presence of microbial volatiles. Our results were strongly supported by data obtained using a highly sensitive method for confocal fluorescence microscopic visualization of iodine stained starch granules. Using Arabidopsis leaves from WT plants, aps1 plants, ss3/ss4 plants lacking both class III and class IV SS, gbss plants lacking the granule-bound SS, and sus1/sus2/sus3/sus4 plants lacking four genes that code for proteins with sucrose synthase activity, in this work we precisely describe the method for preparation of plant samples for starch microscopic examination. Furthermore, we show that this method can be used to visualize glycogen in bacteria, and pure starch granules, amylose and amylopectin.     

A method combining solvent and gel extraction for isolation and preliminary purification of steroids in tissues

A method for the combined extraction and purification of steroids from testicular tissue is described. The tissue is homogenized and extracted with n-hexane/isopropyl alcohol, and the column to which a Sep-Pak C18 cartridge is attached. Following a wash of the Lipidex/Sep-Pak beds with water to remove inorganic and polar organic substances, steroids are eluted with 85% aqueous methanol. Most of the nonpolar lipids and phospholipids remain on the Lipidex/Sep-Pak. The steroid fraction is acidified with acetic acid, diluted to 70% methanol, and passed through a small bed of Lipidex 5000 to remove cholesterol. Recoveries of testosterone and progesterone are about 90%.     

Correlation for the partition behavior of proteins in aqueous two-phase systems: effect of surface hydrophobicity and charge

Correlations to describe the effect of surface hydrophobicity and charge of proteins with their partition coefficient in aqueous two-phase systems were investigated. Polyethylene glycol (PEG) 4000/phosphate, sulfate, citrate, and dextran systems in the presence of low (0.6% w/w) and high (8.8% w/w) levels of NaCl were selected for a systematic study of 12 proteins. The surface hydrophobicity of the proteins was measured by ammonium sulfate precipitation as the inverse of their solubility. The hydrophobicity values measured correlated well with the partition coefficients, K, obtained in the PEG/salt systems at high concentration of NaCl (r = 0.92-0.93). In PEG/citrate systems the partition coefficient correlated well with protein hydrophobicity at low and high concentrations of NaCl (r = 0.81 and 0.93, respectively). The PEG/citrate system also had a higher hydrophobic resolution than other systems to exploit differences in the protein's hydrophobicity. The surface charge and charge density of the proteins was determined over a range of pH (3-9) by electrophoretic titration curves; PEG/salt systems did not discriminate well between proteins of different charge or charge density. In the absence of NaCl, K decreased slightly with increased positive charge. At high NaCl concentration, K increased as a function of positive charge. This suggested that the PEG-rich top phase became more negative as the concentration of NaCl in the systems increased and, therefore, attracted the positively charged proteins. The effect of charge was more important in PEG/dextran systems at low concentrations of NaCl. In the PEG/dextran systems at lower concentration of NaCl, molecular weight appeared to be the prime determinant of partition, whereas no clear effect of molecular weight could be found in PEG/salt systems.     

A rapid method for determination of nitrate in soil and plant extracts

A rapid colourimetric method of determination of nitrate was modified. Proposed modifications eliminated the use of barium sulphate and introduced diazotization of sulphanilamide by the nitrite ion obtained by the reduction of nitrate and subsequent coupling with N-1-naphthyethelenediamine dihydrochloride. Introduction of filtration in place of centrifugation of coloured solution simplified the procedure. Determinations were highly reproducible with coefficient of variation of 2.2 and 2.9% for soil and plant extracts respectively.     

An easy‐to‐run method for routine analysis of eumelanin and pheomelanin in pigmented tissues

A procedure for analysis of melanin‐pigmented tissues based on alkaline hydrogen peroxide degradation coupled with high‐performance liquid chromatography (HPLC) ultraviolet determination of pyrrole‐2,3,5‐tricarboxylic acid (PTCA) for eumelanin and 6‐(2‐amino‐2‐carboxyethyl)‐2‐carboxy‐4‐hydroxybenzothiazole (BTCA) and 1,3‐thiazole‐2,4,5‐tricarboxylic acid for pheomelanin was recently developed. Despite advantages related to the degradation conditions and sample handling, a decrease of the reproducibility and resolution was observed after several chromatographic runs. We report herein an improved chromatographic methodology for simultaneous determination of PTCA and BTCA as representative markers of eumelanin and pheomelanin, respectively, based on the use of an octadecylsilane column with polar end‐capping with 1% formic acid (pH 2.8)/methanol as the eluant. The method requires conventional HPLC equipments and gives very good peak shapes and resolution, without need of ion pair reagents or high salt concentrations in the mobile phase. The intra‐assay precision of the analytical runs was satisfactory with CV values ≤4.0% (n = 5) for the two markers which did not exceed 8% after 50 consecutive injections on the column over 1 week. The peak area ratios at 254 and 280 nm (A₂₈₀/A₂₅₄: PTCA = 1.1, BTCA = 0.6) proved a valuable parameter for reliable identification of the structural markers even in the most complex degradation mixtures. The method can be applied to various eumelanin and pheomelanin pigmented tissues, including mammalian hair, skin and irides, and is amenable to be employed in population screening studies.     

A simple and efficient method for isolation of DNA in high mucilaginous plant tissues

A protocol is described for rapid DNA isolation from Malvaceae plant species and different tissues of Bixaceae that contain large amounts of polysaccharides, polyphenols, and pigments that interfere with DNA extractions. The method is a modification of Dellaporta et al. The current protocol is simple, and no phenolchloroform extraction, ethanol, or isopropranol precipitation is required. The method is based in the incubation of soluble DNA with silica, mix in batch during the extraction. The procedure can be completed in 2 h and many samples can be processed at the same time. DNA of excellent quality was recovered and used for polymerase chain reaction (PCR) amplification, restriction enzyme digestion, and Southern blot analysis. The method was used with healthy Bixa orellana and virus-infected Malvaceae plants.     

A rapid analytical method for monitoring the enantiomeric purity of chiral molecules synthesized in ionic liquid solvents

Ionic liquids (ILs) have been widely used as reaction solvents in asymmetric synthesis due to their interesting physical and chemical properties. However, monitoring reactant-to-product conversion and the enantiopurity of formed stereoisomers often involves a tedious extraction step before chromatographic analysis. In this study, a rapid and sensitive sampling method using headspace solid-phase microextraction (SPME) coupled to chiral gas chromatography was developed for the "on-line" analysis of chiral molecules in the IL solvent. Three different SPME sorbent coatings, namely polydimethylsiloxane, polyacrylate, and a polymeric ionic liquid-based fiber, were examined in this study. The analytical performance of the developed method was evaluated in terms of reproducibility, slope of calibration curve, linear range, calibration linearity, and the determination of detection limits. The SPME method was successfully applied in the determination of enantiomeric excess from selected mixtures of chiral molecules. A preliminary study was performed using an "on-fiber" derivatization approach revealing that the stereoisomers extracted by the SPME fiber can be efficiently derivatized using a short "on-fiber" derivatization step. The developed SPME method eliminates the need of sequestering the reaction, separating the compounds of interest from the IL solvent, and the addition of a derivatizing reagent.     

A rapid survey method for the estimation of density and cover in desert plant communities

Abstract. The Log-series survey method allows rapid estimates of density and cover and is applicable for studies of perennial vegetation in arid environments. An optical rangefinder is used to determine boundaries of large circular plots. Numbers of individuals of each species within a plot are assessed; this information is used to assign species to logarithmic density classes equivalent to the logarithm base 2 of actual abundances. Each species is then assigned to a logarithmic canopy cover class, equivalent to the logarithmbase 2 of average cover per individual. Log total cover per species per plot is obtained by the addition of logarithmic density and cover classes. Percent cover per species is rapidly computed by taking the antilog of the difference between log total cover per species and log total plot area.     

Combinatorial de novo design and application of a biomimetic affinity ligand for the purification of human anti‐HIV mAb 4E10 from transgenic tobacco

Monoclonal anti‐HIV antibody 4E10 (mAb 4E10) is one of the most broadly neutralizing antibodies against HIV, directed against a specific epitope on envelope protein gp41. In the present study, a combinatorial de novo design approach was used for the development of a biomimetic ligand for the affinity purification of mAb 4E10 from tobacco transgenic extract in a single chromatographic step. The biomimetic ligand (4E10lig) was based on a L ‐Phe/β‐Ala bi‐substituted 1,3,5‐triazine (Trz) scaffold (β‐Ala‐Trz‐L ‐Phe, 4E10lig) which potentially mimics the more pronounced electrostatic and hydrophobic interactions of mAb 4E10‐binding sequence determined by screening of a random peptide library. This library was comprised of Escherichia coli cells harboring a plasmid (pFlitrx) engineered to express a fusion protein containing random dodecapeptides that were inserted into the active loop of thioredoxin, which itself was inserted into the dispensable region of the flagellin gene. Adsorption equilibrium studies with this biomimetic ligand and mAb 4E10 determined a dissociation constant (K_D) of 0.41 ± 0.05 µM. Molecular modeling studies of the biomimetic ligand revealed that it can potentially occupy the same binding site as the natural binding core peptide epitope. The biomimetic affinity adsorbent was exploited in the development of a facile mAb 4E10 purification protocol, affording mAb 4E10 of high purity (approximately 95%) with good overall yield (60–80%). Analysis of the antibody preparation by SDS‐PAGE, enzyme‐linked immunosorbent assays (ELISA), and western blot showed that the mAb 4E10 was fully active and free of degraded variants, polyphenols, and alkaloids. Copyright © 2009 John Wiley & Sons, Ltd.     

Assaying CO2 release for determination of formate dehydrogenase activity in entrapment matrices and aqueous-organic two-phase systems

Formate dehydrogenase is an important enzyme for NADH-regeneration in enzyme-catalysed reductions. Methods to determine the activity of this biocatalyst during reaction in aqueous-organic two-phase systems or after immobilisation were therefore investigated. Determination of gaseous CO2 in the headspace of reaction vessels either by gas chromatography or by pressure sensors was found to be a suitable way for deduction of FDH-activity in either of these reaction systems. In the presence of organic solvents, gas chromatography yielded more precise data than pressure sensors, while pressure measurements offer the opportunity to assay continuously the activity of entrapped FDH throughout the whole course of reaction.     

Comparative studies on enzyme preparations and role of cell components for (R)-phenylacetylcarbinol production in a two-phase biotransformation

Whole cell pyruvate decarboxylase (PDC) from Candida utilis enhanced the enzymatic production of (R)-phenylacetylcarbinol (PAC) in an aqueous/octanol biotransformation compared to the partially purified PDC especially for a lower range of initial activities (0.3-2.5 U/mL). With an initial activity of 1.1 U/mL and at a 1:1 phase volume ratio, whole cell PDC achieved a maximum specific PAC production of 42 mg/U (2.8 g/L/h) in comparison to 13 mg/U (0.9 g/L/h) for partially purified PDC. The enhanced performance of whole cell PDC was associated with high stability towards the substrate benzaldehyde. The strong PDC inactivation by benzaldehyde was minimal even when whole cells were broken as long as cell debris was not removed from the broken cells. Biotransformations with various cellular components added to partially purified PDC revealed that membrane components especially 2 mg/mL phosphatidylcholine enhanced PAC concentrations. The role of surfactants was further confirmed from the results with synthetic surfactant sodium bis(2-ethyl-1-hexyl)sulfosuccinate (AOT). It was apparent that the membrane components in whole cells were sufficient for optimal PAC production and no further surfactant addition is required for optimal performance.     

A rapid and robust sequence-based genotyping method for BoLA-DRB3 alleles in large numbers of heterozygous cattle

The BoLA-DRB3 gene is a highly polymorphic major histocompatibility complex class II gene of cattle with over one hundred alleles reported. Most of the polymorphisms are located in exon 2, which encodes the peptide-binding cleft, and these sequence differences play a role in variability of immune responsiveness and disease resistance. However, the high degree of polymorphism in exon 2 leads to difficulty in accurately genotyping cattle, especially heterozygous animals. In this study, we have improved and simplified an earlier sequence-based typing method to easily and reliably genotype cattle for BoLA-DRB3. In contrast to the earlier method, which used a nested primer set to amplify exon 2 followed by sequencing with internal primers, the new method uses only internal primers for both amplification and sequencing, which results in high-quality sequence across the entire exon. The haplofinder software, which assigns alleles from the heterozygous sequence, now has a pre-processing step that uses a consensus of all known alleles and checks for errors in base calling, thus improving the ability to process large numbers of samples. In addition, advances in sequencing technology have reduced the requirement for manual editing and improved the clarity of heterozygous base calls, resulting in longer and clearer sequence reads. Taken together, this has resulted in a rapid and robust method for genotyping large numbers of heterozygous samples for BoLA-DRB3 polymorphisms. Over 400 Holstein-Charolais cattle have now been genotyped for BoLA-DRB3 using this approach.