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1.  A Microfluidic Device for Continuous-Flow Magnetically Controlled Capture and Isolation of Microparticles 
This paper presents a novel microfluidic device that exploits magnetic manipulation for integrated capture and isolation of microparticles in continuous flow. The device, which was fabricated from poly(dimethylsiloxane) (PDMS) by soft-lithography techniques, consists of an incubator and a separator integrated on a single chip. The incubator is based on a novel scheme termed target acquisition by repetitive traversal (TART), in which surface-functionalized magnetic beads repetitively traverse a sample to seek out and capture target particles. This is accomplished by a judicious combination of a serpentine microchannel geometry and a time-invariant magnetic field. Subsequently, in the separator, the captured target particles are isolated from nontarget particles via magnetically driven fractionation in the same magnetic field. Due to the TART incubation scheme that uses a corner-free serpentine channel, the device has no dead volume and allows minimization of undesired particle or magnetic-bead retention. Single-chip integration of the TART incubator with the magnetic-fractionation separator further allows automated continuous isolation and retrieval of specific microparticles in an integrated manner that is free of manual off-chip sample incubation, as often required by alternative approaches. Experiments are conducted to characterize the individual incubation and separation components, as well as the integrated device. The device is found to allow 90% of target particles in a sample to be captured and isolated and 99% of nontarget particles to be eliminated. With this high separation efficiency, along with excellent reliability and flexibility, the device is well suited to sorting, purification, enrichment, and detection of micro/nanoparticles and cells in lab-on-a-chip systems.
PMCID: PMC3916004  PMID: 24511214
Cell sorting; magnetic manipulation; micro-fluidics; on-chip incubation; particle separation
2.  P176-M Rapid Purification and Enrichment of Proteins from Crude Solutions Using Reversed Phase Microparticles and Subsequent Generation of Peptide Mass Fingerprints by MALDI-TOF Mass Spectrometry 
The generation of peptide mass fingerprints followed by a database search is a common tool for the mass spectrometric identification of proteins. To provide a high sensitivity, proteins must be efficiently purified and concentrated prior to enzymatic digestion. Common desalting procedures, like ultrafiltration or dialysis, are very time consuming and work best for high protein concentrations. Another critical point is the proteolysis of the investigated protein, which works efficiently only with concentrated protein solutions. Therefore, efficient concentration and simultaneous purification using solid phase extraction (SPE) will be the method of choice to receive pure and highly concentrated protein solutions prior to enzymatic digestion. In this work, we manufactured magnetic reversed phase particles for the efficient purification and simultaneous concentration of protein samples with volumes up to several millilitres. The SPE procedure was compared with dialysis using commercial available microconcentrators with a cut-off membrane. Due to the magnetic core, each washing and elution step could be performed within 15 minutes. Then, the bound protein was digested directly on the beads, resulting in a remarkable increase of protein detection and better mass structural analysis. Useful MOWSE scores were achieved using bovine serum albumin as a model protein with concentrations as low as 50 ng/ml (720 pM). Compared to the dialysis procedure, which needs several hours, the isolation and purification of protein can be performed in minutes with the reversed phase particles.
PMCID: PMC2291834
3.  A proteomic view on the developmental transfer of homologous 30 kDa lipoproteins from peripheral fat body to perivisceral fat body via hemolymph in silkworm, Bombyx mori 
BMC Biochemistry  2012;13:5.
A group of abundant proteins of ~30 kDa is synthesized in silkworm larval peripheral fat body (PPFB) tissues and transported into the open circulatory system (hemolymph) in a time-depended fashion to be eventually stored as granules in the pupal perivisceral fat body (PVFB) tissues for adult development during the non-feeding stage. These proteins have been shown to act anti-apoptotic besides being assigned roles in embryogenesis and defense. However, detailed protein structural information for individual PPFB and PVFB tissues during larval and pupal developmental stages is still missing. Gel electrophoresis and chromatography were used to separate the 30 kDa proteins from both PPFB and PVFB as well as hemolymph total proteomes. Mass spectrometry (MS) was employed to elucidate individual protein sequences. Furthermore, 30 kDa proteins were purified and biochemically characterized.
One- and two-dimensional gel electrophoresis (1/2D-PAGE) was used to visualize the relative changes of abundance of the 30 kDa proteins in PPFB and PVFB as well as hemolymph from day 1 of V instar larval stage to day 6 of pupal stage. Their concentrations were markedly increased in hemolymph and PVFB up to the first two days of pupal development and these proteins were consumed during development of the adult insect. Typically, three protein bands were observed (~29, 30, 31 kDa) in 1D-PAGE, which were subjected to MS-based protein identification along with spots excised from 2D-gels run for those proteomes. Gas phase fragmentation was used to generate peptide sequence information, which was matched to the available nucleotide data pool of more than ten highly homologous insect 30 kDa lipoproteins. Phylogenetic and similarity analyses of those sequences were performed to assist in the assignment of experimentally identified peptides to known sequences. Lipoproteins LP1 to LP5 and L301/302 could be matched to peptides extracted from all bands suggesting the presence of full length and truncated or modified protein forms in all of them. The individual variants could not be easily separated by classical means of purification such as 2D-PAGE because of their high similarity. They even seemed to aggregate as was indicated by native gel electrophoresis. Multistep chromatographic procedures eventually allowed purification of an LP3-like protein. The protein responded to lipoprotein-specific staining.
In B. mori larvae and pupae, 30 kDa lipoproteins LP1 to LP5 and L301/302 were detected in PPFB and PVFB tissue as well as in hemolymph. The concentration of these proteins changed progressively during development from their synthesis in PPFB, transport in hemolymph to storage in PVFB. While the 30 kDa proteins could be reproducibly separated in three bands electrophoretically, the exact nature of the individual protein forms present in those bands remained partially ambiguous. The amino acid sequences of all known 30 kDa proteins showed very high homology. High-resolution separation techniques will be necessary before MS and other structural analysis can shed more light on the complexity of the 30 kDa subproteome in B. mori. A first attempt to that end allowed isolation of a B. mori LP3-like protein, the complete structure, properties and function of which will now be elucidated in detail.
PMCID: PMC3306753  PMID: 22369700
4.  Characterization and Purification of Polydisperse Reconstituted Lipoproteins and Nanolipoprotein Particles 
Heterogeneity is a fact that plagues the characterization and application of many self-assembled biological constructs. The importance of obtaining particle homogeneity in biological assemblies is a critical goal, as bulk analysis tools often require identical species for reliable interpretation of the results—indeed, important tools of analysis such as x-ray diffraction typically require over 90% purity for effectiveness. This issue bears particular importance in the case of lipoproteins. Lipid-binding proteins known as apolipoproteins can self assemble with liposomes to form reconstituted high density lipoproteins (rHDLs) or nanolipoprotein particles (NLPs) when used for biotechnology applications such as the solubilization of membrane proteins. Typically, the apolipoprotein and phospholipids reactants are self assembled and even with careful assembly protocols the product often contains heterogeneous particles. In fact, size polydispersity in rHDLs and NLPs published in the literature are frequently observed, which may confound the accurate use of analytical methods. In this article, we demonstrate a procedure for producing a pure, monodisperse NLP subpopulation from a polydisperse self-assembly using size exclusion chromatography (SEC) coupled with high resolution particle imaging by atomic force microscopy (AFM). In addition, NLPs have been shown to self assemble both in the presence and absence of detergents such as cholate, yet the effects of cholate on NLP polydispersity and separation has not been systematically examined. Therefore, we examined the separation properties of NLPs assembled in both the absence and presence of cholate using SEC and native gel electrophoresis. From this analysis, NLPs prepared with and without cholate showed particles with well defined diameters spanning a similar size range. However, cholate was shown to have a dramatic affect on NLP separation by SEC and native gel electrophoresis. Furthermore, under conditions where different sized NLPs were not sufficiently separated or purified by SEC, AFM was used to deconvolute the elution pattern of different sized NLPs. From this analysis we were able to purify an NLP subpopulation to 90% size homogeneity by taking extremely fine elutions from the SEC. With this purity, we generate high quality NLP crystals that were over 100 μm in size with little precipitate, which could not be obtained utilizing the traditional size exclusion techniques. This purification procedure and the methods for validation are broadly applicable to other lipoprotein particles.
PMCID: PMC2738905  PMID: 19742178
apolipoproteins; nanolipoprotein particles; bilayer mimetic; nanobiotechnology; atomic force microscopy; size-exclusion chromatography; lipoprotein crystallization
5.  Defining the budding yeast chromatin-associated interactome 
We report here the first large-scale affinity purification and mass spectrometry (AP-MS) study of chromatin-associated protein, in which over 100 different baits involved in chromatin biology were studied by modified chromatin immunopurification (mChIP)-MS. In particular, focus was placed on poorly studied chromatin binding proteins, such as transcription factors, which have been underrepresented in previous AP-MS studies.mChIP-MS analysis of transcription factors identified dense networks of protein associated with chromatin that were composed of specific transcriptional co-activators, information not accessible through the use of classical AP-MS methods.Finally, we demonstrate that novel protein–protein interactions identified in study by mChIP have functional implications exemplified by the detailed study of both the ubiquitination of the proline isomerase Cpr1 and of histone chaperones involved in the regulation of the HTA1-HTB1 promoter.Our work demonstrates the value of targeted interactome studies, in which affinity purification methods are adapted to the needs of specific baits, as is the case for chromatin binding proteins.
The maintenance of cellular fitness requires living organisms to integrate multiple signals into coordinated outputs. Central to this process is the regulation of the expression of the genetic information encoded into DNA. As a result, there are numerous constraints imposed on gene expression. The access to DNA is restricted by the formation of nucleosomes, in which DNA is wrapped around histone octamers to form chromatin wherein the volume of DNA is considerably reduced. As such, nucleosome positioning is critical and must be defined precisely, particularly during transcription (Workman, 2006). Furthermore, nucleosomes can be actively assembled/disassembled by histone chaperones and can be made to ‘slide' along DNA by the actions of chromatin remodelers. Moreover, the histone proteins are heavily regulated at the expression level and by extensive post-translational modifications (PTMs) (Campos and Reinberg, 2009). Histone PTMs have also been shown to help recruit numerous chromatin-associated factors in accordance with the histone code (Strahl and Allis, 2000). Although our understanding of chromatin and its roles has improved, we still have limited knowledge of the chromatin-associated protein complexes and their interactions.
The characterization of biological systems and of specific subdomain within them, such as chromatin, remains a difficult task. An efficient approach to gain insight in the function of protein is to define its interactome. The underlying principle of protein interaction mapping is that proteins found to interact must be involved in common processes and localization, i.e., guilt by association. The large-scale mapping of proteins interactions allows to annotate protein of unknown functions, implicate protein of known functions in different processes and derive new hypothesis. This is possible because most proteins do not act in isolation but rather as part of complexes, and thus possess interaction partners that can now be detected with the right tools. AP-MS has emerged as a powerful tool for characterizing protein–protein interactions and biological systems in general (Gingras et al, 2007; Gstaiger and Aebersold, 2009).
Recently, we reported the development of a novel affinity purification approach termed mChIP, which was designed to improve the characterization of DNA binding proteins interactome (Lambert et al, 2009). The mChIP method consists of a single affinity purification step, whereby chromatin-associated proteins are isolated from mildly sonicated and gently clarified cellular extracts using magnetic beads coated with antibodies (Lambert et al, 2009; Figure 1A). As such, the mChIP approach maintains chromatin fragments in solution enabling their specific purification, something not previously possible in classical AP-MS methods (Lambert et al, 2009).
In this study, we report the utilization of mChIP followed by MS for the characterization of more than 100 proteins and their associated protein networks (Figure 1B). We initially focused on DNA-associated proteins that had been poorly characterized in past AP-MS studies, such as transcription factors. In addition, many histone modifiers, such as lysine acetyl transferases (KAT) and lysine methyl transferases, critical components of chromatin function and regulation, were also studied by mChIP. This resulted in raw non-redundant mChIP-MS data containing ∼9000 protein–protein interactions between ∼900 proteins. Following a two-step curation process designed to remove common contaminants and protein not specifically associated with the baits under study, a high confidence mChIP-MS data set was produced containing 2966 protein–protein interactions between 724 proteins (Figure 1B). It is important to note that our curation strategy was capable of maintaining the majority of the protein–protein interaction identified in previous AP-MS studies, while removing the bulk of protein–protein interaction not related to chromatin biology. Further analysis of the mChIP-MS data set revealed that for most bait tested, mChIP-MS resulted in the identification of more interaction partners than classical TAP-MS.
Visualization of the mChIP-MS data set was achieved by generating heat maps from two-dimensional hierarchical clustering of the bait–prey interactions. This revealed numerous clusters within our data set supporting functional relationship. For instance, mChIP analysis of the highly homologous heat-shock-inducible transcription factors Msn2 and Msn4 clustered with different transcriptional co-activators. Importantly, our analysis also revealed key differences in the co-activators associated with Msn2 and Msn4 relevant to their function. Another example that we explore in greater details is the Cpr1 proline isomerase, a known member of the Set3 complex (Pijnappel et al, 2001). mChIP-MS analysis of Cpr1 revealed an extended network of associated proteins, including the E3 ubiquitin ligase Bre1 and its association partner Lge1 (Figure 5A). This association raised the possibility of a direct action of Bre1/Lge1 on Cpr1 to ubiquitinate it. In targeted experiments, we observed that Cpr1 is in fact ubiquitinated in a process involving Bre1/Lge1 (Figure 5E), confirming their functional relationship. As such, mChIP is capable of uncovering novel protein–protein interactions with physiological impacts.
In this study, we report how the use of an AP-MS method designed for a given class of protein (chromatin-associated proteins) can help uncover numerous novel protein–protein interactions. Furthermore, our work detected dense chromatin-associated protein networks being co-purified with multiple transcription factors and other DNA binding proteins. The fact that even in the best-characterized model organism Saccharomyces cerevisiae, thousands of novel protein–protein interactions can be detected supports our view that targeted interactome studies are worthwhile and desirable. As such, the budding yeast interactome can still be consider incomplete and warrant further study.
We previously reported a novel affinity purification (AP) method termed modified chromatin immunopurification (mChIP), which permits selective enrichment of DNA-bound proteins along with their associated protein network. In this study, we report a large-scale study of the protein network of 102 chromatin-related proteins from budding yeast that were analyzed by mChIP coupled to mass spectrometry. This effort resulted in the detection of 2966 high confidence protein associations with 724 distinct preys. mChIP resulted in significantly improved interaction coverage as compared with classical AP methodology for ∼75% of the baits tested. Furthermore, mChIP successfully identified novel binding partners for many lower abundance transcription factors that previously failed using conventional AP methodologies. mChIP was also used to perform targeted studies, particularly of Asf1 and its associated proteins, to allow for a understanding of the physical interplay between Asf1 and two other histone chaperones, Rtt106 and the HIR complex, to be gained.
PMCID: PMC3018163  PMID: 21179020
affinity purification; chromatin-associated protein networks; mass spectrometry; nucleosome assembly factor Asf1; protein–DNA interaction
6.  One-step isolation of plasma membrane proteins using magnetic beads with immobilized concanavalin A1 
We have developed a simple method for isolating and purifying plasma membrane proteins from various cell types. This one-step affinity-chromatography method uses the property of the lectin concanavalin A (ConA) and the technique of magnetic-bead separation to obtain highly purified plasma membrane proteins from crude membrane preparations or cell lines. ConA is immobilized onto magnetic beads by binding biotinylated ConA to streptavidin magnetic beads. When these ConA magnetic beads were used to enrich plasma membranes from a crude membrane preparation, this procedure resulted in 3.7-fold enrichment of plasma membrane marker 5′-nucleotidase activity with 70% recovery of the activity in the crude membrane fraction of rat liver. In agreement with the results of 5′-nucleotidase activity, immunoblotting with antibodies specific for a rat liver plasma membrane protein, CEACAM1, indicated that CEACAM1 was enriched about threefold relative to that of the original membranes. In similar experiments, this method produced 13-fold enrichment of 5′-nucleotidase activity with 45% recovery of the activity from a total cell lysate of PC-3 cells and 7.1-fold enrichment of 5′-nucleotidase activity with 33% recovery of the activity from a total cell lysate of HeLa cells. These results suggest that this one-step purification method can be used to isolate total plasma membrane proteins from tissue or cells for the identification of membrane biomarkers.
PMCID: PMC2600885  PMID: 18765283
7.  Characterization of Molecules Binding to the 70K N-terminal Region of Fibronectin by IFAST Purification Coupled with Mass Spectrometry 
Journal of proteome research  2013;12(7):10.1021/pr400225p.
Fibronectin (Fn) is a large glycoprotein present in plasma and extracellular matrix and is important for many processes. Within Fn the 70kDa N-terminal region (70k-Fn) is involved in cell-mediated Fn assembly, a process that contributes to embryogenesis, development, and platelet thrombus formation. In addition, major human pathogens including Staphlycoccus aureus and Streptococcus pyogenes, bind the 70k-Fn region by a novel form of protein-protein interaction called β-zipper formation, facilitating bacterial spread and colonization. Knowledge of blood plasma and platelet proteins that interact with 70k-Fn by β-zipper formation is incomplete. In the current study, we aimed to characterize these proteins through affinity purification. For this affinity purification, we used a novel purification technique termed immiscible filtration assisted by surface tension (IFAST). The foundation of this technology is immiscible phase filtration, using a magnet to draw paramagnetic particle (PMP)-bound analyte through an immiscible barrier (oil or organic solvent) that separates an aqueous sample from an aqueous eluting buffer. The immiscible barrier functions to remove unbound proteins via exclusion rather than dilutive washing used in traditional isolation methods. We identified 31 interactors from plasma, of which only seven were previously known to interact with Fn. Furthermore, five proteins were identified to interact with 70k-Fn from platelet lysate, of which one was previously known. These results demonstrate that IFAST offers advantages for proteomic studies of interacting molecules in that the technique requires small sample volumes, can be done with high enough throughput to sample multiple interaction conditions, and is amenable to exploratory mass spectrometric and confirmatory immuno-blotting read-outs.
PMCID: PMC3832424  PMID: 23750785
Fibronectin; IFAST; Interactome; Myosin Heavy Chain-9; Gelsolin
8.  Application of magnetic techniques in the field of drug discovery and biomedicine 
Magnetic separation technology, using magnetic particles, is quick and easy method for sensitive and reliable capture of specific proteins, genetic material and other biomolecules. The technique offers an advantage in terms of subjecting the analyte to very little mechanical stress compared to other methods. Secondly, these methods are non-laborious, cheap and often highly scalable. Moreover, techniques employing magnetism are more amenable to automation and miniaturization. Now that the human genome is sequenced and about 30,000 genes are annotated, the next step is to identify the function of these individual genes, carrying out genotyping studies for allelic variation and SNP analysis, ultimately leading to identification of novel drug targets. In this post-genomic era, technologies based on magnetic separation are becoming an integral part of todays biology laboratory. This article briefly reviews the selected applications of magnetic separation techniques in the field of biotechnology, biomedicine and drug discovery.
PMCID: PMC212320  PMID: 14521720
9.  P183-T Analysis of Glycoproteins in Human Serum by Means of Glyco-Specific Magnetic Bead Separation and LC-MALDI with Automated Glycopeptide Detection 
Comprehensive proteomic analyses require efficient and selective pre-fractionation to facilitate analysis of post-translationally modified peptides and proteins and automated analysis procedures for the detection, identification, and structural characterization of the corresponding peptide modification.
Selective capturing of glycopeptides and -proteins was attained by means of magnetic particles specifically functionalized with lectins or boronic acids that bind to various structural motifs. Human serum contains a high number of glycoproteins, comprising several orders of magnitude in concentration. Thereby, isolation and subsequent identification of low-abundant glycoproteins from serum is a challenging task.
Human serum was incubated with differentially functionalized magnetic micro-particles (lectins or boronic acids). Isolated proteins were released from the beads under acidic conditions, dried, and subsequently re-dissolved and digested with trypsin. The resulting complex mixture of peptides was subjected to LC-MALDI analysis. The respective glycoproteins were identified by direct MS/MS analysis and subsequent database searching. Intact glyco-peptides enriched by a second magnetic-bead purification on peptide level were directly subjected to LC-MALDI analysis to get structural information about the glycan and peptide parts. A precondition to this novel approach was the discovery of certain consensus peak patterns in the MALDI-MS/MS spectra, allowing the automatic determination of the peptide part and the glycosidic information of the glycopeptides supported by bioinformatics tools.
Applying this fast and simple approach, a high number of low-abundant proteins were identified, comprising known or predicted glycosylation sites. According to the specific binding preferences of the different types of beads, complementary results were obtained from experiments using magnetic ConA, LCA, WGA, jacalin, and boronic acid beads, respectively. The use of jacalin and boronic acid beads facilitates the enrichment of O-glycosidically modified proteins. In contrast, ConA, WGA, and LCA specifically bind N-glycosylated peptides and proteins. Few non-glycosylated proteins were identified, probably due to co-precipitation with glycosylated proteins.
PMCID: PMC2291947
10.  Analytical and preparative applications of magnetic split-flow thin fractionation on several ion-labeled red blood cells 
Magnetic Split-flow thin (SPLITT) fractionation is a newly developed technique for separating magnetically susceptible particles. Particles with different field-induced velocities can be separated into two fractions by adjusting applied magnetic forces and flow-rates at inlets and outlets.
Magnetic particles, Dynabeads, were used to test this new approach of field-induced velocity for susceptibility determination using magnetic SF at different magnetic field intensities. Reference measurements of magnetic susceptibility were made using a superconducting quantum interference device (SQUID) magnetometer. Various ion-labeled red blood cells (RBC) were used to study susceptibility determination and throughput parameters for analytical and preparative applications of magnetic SPLITT fractionation (SF), respectively. Throughputs were studied at different sample concentrations, magnetic field intensities, and channel flow-rates.
The susceptibilities of Dynabeads determined by SPLITT fractionation (SF) were consistent with those of reference measurement using a superconducting quantum interference device (SQUID) magnetometer. Determined susceptibilities of ion-labeled RBC were consistent within 9.6% variations at two magnetic intensities and different flow-rates. The determined susceptibilities differed by 10% from referenced measurements. The minimum difference in magnetic susceptibility required for complete separation was about 5.0 × 10-6 [cgs]. Sample recoveries were higher than 92%. The throughput of magnetic SF was approximately 1.8 g/h using our experimental setup.
Magnetic SF can provide simple and economical determination of particle susceptibility. This technique also has great potential for cell separation and related analysis. Continuous separations of ion-labeled RBC using magnetic SF were successful over 4 hours. The throughput was increased by 18 folds versus early study. Sample recoveries were 93.1 ± 1.8% in triplicate experiments.
PMCID: PMC1779266  PMID: 17177988
11.  Use of anionic denaturing detergents to purify insoluble proteins after overexpression 
BMC Biotechnology  2012;12:95.
Many proteins form insoluble protein aggregates, called “inclusion bodies”, when overexpressed in E. coli. This is the biggest obstacle in biotechnology. Ever since the reversible denaturation of proteins by chaotropic agents such as urea or guanidinium hydrochloride had been shown, these compounds were predominantly used to dissolve inclusion bodies. Other denaturants exist but have received much less attention in protein purification. While the anionic, denaturing detergent sodiumdodecylsulphate (SDS) is used extensively in analytical SDS-PAGE, it has rarely been used in preparative purification.
Here we present a simple and versatile method to purify insoluble, hexahistidine-tagged proteins under denaturing conditions. It is based on dissolution of overexpressing bacterial cells in a buffer containing sodiumdodecylsulfate (SDS) and whole-lysate denaturation of proteins. The excess of detergent is removed by cooling and centrifugation prior to affinity purification. Host- and overexpressed proteins do not co-precipitate with SDS and the residual concentration of detergent is compatible with affinity purification on Ni/NTA resin. We show that SDS can be replaced with another ionic detergent, Sarkosyl, during purification. Key advantages over denaturing purification in urea or guanidinium are speed, ease of use, low cost of denaturant and the compatibility of buffers with automated FPLC.
Ionic, denaturing detergents are useful in breaking the solubility barrier, a major obstacle in biotechnology. The method we present yields detergent-denatured protein. Methods to refold proteins from a detergent denatured state are known and therefore we propose that the procedure presented herein will be of general application in biotechnology.
PMCID: PMC3536628  PMID: 23231964
Inclusion Bodies; Sodiumdodecylsulphate (SDS); N-lauroylsarcosine sodium salt (Sarkosyl); Immobilized Metal Ion Affinity Chromatography (IMAC)
12.  Purification of Specific Cell Population by Fluorescence Activated Cell Sorting (FACS) 
Experimental and clinical studies often require highly purified cell populations. FACS is a technique of choice to purify cell populations of known phenotype. Other bulk methods of purification include panning, complement depletion and magnetic bead separation. However, FACS has several advantages over other available methods. FACS is the preferred method when very high purity of the desired population is required, when the target cell population expresses a very low level of the identifying marker or when cell populations require separation based on differential marker density. In addition, FACS is the only available purification technique to isolate cells based on internal staining or intracellular protein expression, such as a genetically modified fluorescent protein marker. FACS allows the purification of individual cells based on size, granularity and fluorescence. In order to purify cells of interest, they are first stained with fluorescently-tagged monoclonal antibodies (mAb), which recognize specific surface markers on the desired cell population (1). Negative selection of unstained cells is also possible. FACS purification requires a flow cytometer with sorting capacity and the appropriate software. For FACS, cells in suspension are passed as a stream in droplets with each containing a single cell in front of a laser. The fluorescence detection system detects cells of interest based on predetermined fluorescent parameters of the cells. The instrument applies a charge to the droplet containing a cell of interest and an electrostatic deflection system facilitates collection of the charged droplets into appropriate collection tubes (2). The success of staining and thereby sorting depends largely on the selection of the identifying markers and the choice of mAb. Sorting parameters can be adjusted depending on the requirement of purity and yield. Although FACS requires specialized equipment and personnel training, it is the method of choice for isolation of highly purified cell populations.
PMCID: PMC3144656  PMID: 20644514
13.  Isolation and Characterization of a Novel Magnetotactic Bacterium From Iran: Iron Uptake and Producing Magnetic Nanoparticles in Alphaproteobacterium MTB-KTN90 
Magnetotactic bacteria (MTB) have the ability to biomineralize unique intracellular magnetic nanosize particles. These bacteria and their magnetosomes are under special attraction because of their great useful potential in nano-biotechnological and biomedical applications. MTB are ubiquitous in aquatic environments, but their isolation and axenic cultivation in pure culture is very difficult and only a limited number of them have been isolated in pure culture.
The main goal of this study was screening, isolation and cultivation of a new strain of these fastidious bacteria in pure culture from Iran to use them and their magnetosomes.
Materials and Methods:
Thirty samples were collected from various aquatic habitats. Most important physicochemical environmental factors that are involved in growth of MTB in the microcosms were investigated using inductively coupled plasma atomic emission spectroscopy (ICP-AES), portable dissolved oxygen meter, etc. Capillary racetrack technique and magnetic separation were used to purify and enrich MTB. Various isolation media were simultaneously used for isolation of a new magnetotactic bacterium in pure culture. Two imaging techniques were used to visualize the characterizations and cell division: transmission electron microscopy (TEM) and field-emission scanning electron microscopy (FESEM). Polymerase chain reaction (PCR), ChromasPro software and MEGA5 were applied for sequence analysis of the 16S rRNA gene.
The results revealed a correlation of important physicochemical factors such as pH and iron with growth and blooms of these bacteria in the microcosms. New strain MTB-KTN90 was isolated in a modified isolation medium at microaerophilic zone from Anzali lagoon, Iran and cultured in a modified growth medium subsequently. The phylogenetic analysis showed that the strain belongs to Alphaproteobacteria. Growth and iron uptake studies indicated an important role by this bacterium in the iron biogeochemical cycle. For the first time, this paper introduced a cultured magnetotactic Alphaproteobacterium, able to synthesize magnetosomes in the temperatures above 30°C and reduce selenate oxyanion.
This paper may serve as a guide to screening, isolation, and cultivation of more new MTB. The new isolated strain opens up good opportunities for biotechnological applications such as medicine to bioremediation processes due to its unique abilities.
PMCID: PMC4255385  PMID: 25485070
Magnetic Nanoparticles; Magnetotactic Bacteria; 16S rRNA Phylogeny; Alphaproteobacteria; Anzali Lagoon
14.  Formation of magnetite by bacteria and its application 
Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein–magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.
PMCID: PMC2475554  PMID: 18559314
magnetotactic bacteria; bacterial magnetic particles; surface modification of magnetite; magnetic separation; protein display; fully automated system
15.  Magnet design for a low-emittance storage ring 
Journal of Synchrotron Radiation  2014;21(Pt 5):884-903.
The magnet design of the MAX IV 3 GeV storage ring replaces the conventional support girder + discrete magnets scheme of previous third-generation light sources with a compact integrated design having several consecutive magnet elements precision-machined out of a common solid iron block.
The MAX IV 3 GeV storage ring, currently under construction, pursues the goal of low electron beam emittance by using a multi-bend achromat magnet lattice, which is realised by having several consecutive magnet elements precision-machined out of a common solid iron block, 2.3–3.4 m long. With this magnet design solution, instead of having 1320 individual magnets, the MAX IV 3 GeV storage ring is built up using 140 integrated ‘magnet block’ units, containing all these magnet elements. Major features of this magnet block design are compactness, vibration stability and that the alignment of magnet elements within each unit is given by the mechanical accuracy of the CNC machining rather than individual field measurement and adjustment. This article presents practical engineering details of implementing this magnet design solution, and mechanical + magnetic field measurement results from the magnet production series. At the time of writing (spring 2014), the production series, which is totally outsourced to industry, is roughly half way through, with mechanical/magnetic QA conforming to specifications. It is the conclusion of the authors that the MAX IV magnet block concept, which has sometimes been described as new or innovative, is from a manufacturing point of view simply a collection of known mature production methods and measurement procedures, which can be executed at fixed cost with a low level of risk.
PMCID: PMC4181640  PMID: 25177980
accelerator; magnet; magnet block; multi-bend achromat; low emittance
16.  Application of Magnetic Particle Tracking Velocimetry to Quadrupole Magnetic Sorting of Porcine Pancreatic Islets 
Biotechnology and bioengineering  2011;108(9):2107-2117.
Magnetic isolation is a promising method for separating and concentrating pancreatic islets of Langerhans for transplantation in Type 1 Diabetes patients. We are developing a continuous magnetic islet sorter to overcome the restrictions of current purification methods that result in limited yield and viability. In Quadrupole Magnetic Sorting (QMS) islets are magnetized by infusing superparamagnetic microbeads into islets’ vasculature via arteries that serve the pancreas. The performance of the islet sorter depends on the resulting speed of the islets in an applied magnetic field, a property known as magnetophoretic mobility. Essential to the design and successful operation of the QMS is a method to measure the magnetophoretic mobilities of magnetically infused islets. We have adapted a Magnetic Particle Tracking Velocimeter (MPTV) to measure the magnetophoretic mobility of particles up to 1000 microns in diameter. Velocity measurements are performed in a well-characterized uniform magnetic energy gradient using video imaging followed by analysis of the video images with a computer algorithm that produces a histogram of absolute mobilities. MPTV was validated using magnetic agarose beads serving as islet surrogates and subjecting them to QMS. Mobility distributions of labeled porcine islets indicated that magnetized islets have sufficient mobility to be captured by the proposed sorting method, with this result confirmed in test isolations of magnetized islets.
PMCID: PMC3139696  PMID: 21495008
Particle tracking velocimetry; magnetic flow sorter; pancreatic islets isolation; magnetic particles
17.  Hofmeister series salts enhance purification of plasmid DNA by non-ionic detergents 
Biotechnology and bioengineering  2011;108(8):1872-1882.
Ion-exchange chromatography is the standard technique used for plasmid DNA purification, an essential molecular biology procedure. Non-ionic detergents (NIDs) have been used for plasmid DNA purification, but it is unclear whether Hofmeister series salts (HSS) change the solubility and phase separation properties of specific NIDs, enhancing plasmid DNA purification. After scaling-up NID-mediated plasmid DNA isolation, we established that NIDs in HSS solutions minimize plasmid DNA contamination with protein. In addition, large-scale NID/HSS solutions eliminated LPS contamination of plasmid DNA more effectively than Qiagen ion-exchange columns. Large-scale NID isolation/NID purification generated increased yields of high quality DNA compared to alkali isolation/column purification. This work characterizes how HSS enhance NID-mediated plasmid DNA purification, and demonstrates that NID phase transition is not necessary for LPS removal from plasmid DNA. Specific NIDs such as IGEPAL CA-520 can be utilized for rapid, inexpensive and efficient laboratory-based large-scale plasmid DNA purification, outperforming Qiagen-based column procedures.
PMCID: PMC3117116  PMID: 21351074
plasmid DNA purification; non-ionic detergents; Hofmeister salts
18.  Development of Novel Magnetic Nanoparticles for Hyperthermia Cancer Therapy 
Proceedings of SPIE  2011;7901:790115-.
Advances in magnetic nanoparticle hyperthermia are opening new doors in cancer therapy. As a standalone or adjuvant therapy this new modality has the opportunity significantly advance thermal medicine. Major advantages of using magnetic magnetite (Fe3O4) nanoparticles are their highly localized power deposition and the fact that the alternating magnetic fields (AMF) used to excite them can penetrate deeply into the body without harmful effect. One limitation, however, which hinders the technology, is the problem of inductive heating of normal tissue by the AMF if the frequency and fields strength are not appropriately matched to the tissue. Restricting AMF amplitude and frequency limits the heat dose which can be selectively applied to cancerous tissue via the magnetic nanoparticle, thus lowering therapeutic effect. In an effort to address this problem, particles with optimized magnetic properties must be developed. Using particles with higher saturation magnetizations and coercivity will enhance hysteresis heating increasing particle power density at milder AMF strengths and frequencies. In this study we used oil in water microemulsions to develop nanoparticles with zero-valent Fe cores and magnetite shells. The superior magnetic properties of zero-valent Fe give these particles the potential for improved SAR over pure magnetite particles. Silane and subsequently dextran have been attached to the particle surface in order to provide a biocompatible surfactant coating. The heating capability of the particles was tested in-vivo using a mouse tumor model. Although we determined that the final stage of synthesis, purification of the dextran coated particles, permits significant corrosion/oxidation of the iron core to hematite, the particles can effectively heat tumor tissue. Improving the purification procedure will allow the generation Fe/Fe3O4 with superior SAR values.
PMCID: PMC3947375  PMID: 24619487
Magnetic Nanoparticle; Ferrofluid; Hyperthermia; Tumor; Cancer; Synthesis
19.  P174-T Affinity Protein Purification by Automation Using a Magtration Robotic System 
Affinity purification is a powerful tool for protein enrichment in proteomics studies. We here present a fully automated system for purification of His-tag proteins and IgG using Ni2+/Co2+ and Protein A magnetic beads, respectively. Reagents for His-tag protein or IgG purification are pre-dispensed in a sealed cartridge for automated runs on a Magtration 12GC robot. The automated purification is based on Magtration technology to perform magnetic bead separation similar to a filtration process in a pipette tip. An optimized protocol has been developed for the automated protein purification. High protein purity and yields were obtained using this automated system. His-tag protein human galectin-1 was purified to approx. 1.6 mg with 12 samples processed in parallel within 30 min on the 12GC robot. This system was also used to screen the expression of His-tag water-soluble proteins and inclusion bodies in bacterial cells, even at a very low expression level. Using Protein A magnetic beads and corresponding pre-filled reagent cartridges, various amounts of human serum (15–80 μL) and the magnetic beads (100–200 mg) were tested on the robotic system. With 30 μL serum and 150 mg magnetic beads, we purified IgG with a high yield of 230 μg. A total of approx. 2.8 mg IgG can be obtained within 60 min with 12 samples run in parallel on the robot. The magnetic beads after the affinity purification can be regenerated by automation for repeated use. Magtration robotic system can be extended for purification of GST-tag fusion proteins and Immunoprecipitation by automation. We have provided an automated protein purification system with a Magtration robot and pre-filled reagent cartridges for rapid and multiparallel processing of different proteins.
PMCID: PMC2291955
20.  Advanced Electrophysiologic Mapping Systems 
Executive Summary
To assess the effectiveness, cost-effectiveness, and demand in Ontario for catheter ablation of complex arrhythmias guided by advanced nonfluoroscopy mapping systems. Particular attention was paid to ablation for atrial fibrillation (AF).
Clinical Need
Tachycardia refers to a diverse group of arrhythmias characterized by heart rates that are greater than 100 beats per minute. It results from abnormal firing of electrical impulses from heart tissues or abnormal electrical pathways in the heart because of scars. Tachycardia may be asymptomatic, or it may adversely affect quality of life owing to symptoms such as palpitations, headaches, shortness of breath, weakness, dizziness, and syncope. Atrial fibrillation, the most common sustained arrhythmia, affects about 99,000 people in Ontario. It is associated with higher morbidity and mortality because of increased risk of stroke, embolism, and congestive heart failure. In atrial fibrillation, most of the abnormal arrhythmogenic foci are located inside the pulmonary veins, although the atrium may also be responsible for triggering or perpetuating atrial fibrillation. Ventricular tachycardia, often found in patients with ischemic heart disease and a history of myocardial infarction, is often life-threatening; it accounts for about 50% of sudden deaths.
Treatment of Tachycardia
The first line of treatment for tachycardia is antiarrhythmic drugs; for atrial fibrillation, anticoagulation drugs are also used to prevent stroke. For patients refractory to or unable to tolerate antiarrhythmic drugs, ablation of the arrhythmogenic heart tissues is the only option. Surgical ablation such as the Cox-Maze procedure is more invasive. Catheter ablation, involving the delivery of energy (most commonly radiofrequency) via a percutaneous catheter system guided by X-ray fluoroscopy, has been used in place of surgical ablation for many patients. However, this conventional approach in catheter ablation has not been found to be effective for the treatment of complex arrhythmias such as chronic atrial fibrillation or ventricular tachycardia. Advanced nonfluoroscopic mapping systems have been developed for guiding the ablation of these complex arrhythmias.
The Technology
Four nonfluoroscopic advanced mapping systems have been licensed by Health Canada:
CARTO EP mapping System (manufactured by Biosense Webster, CA) uses weak magnetic fields and a special mapping/ablation catheter with a magnetic sensor to locate the catheter and reconstruct a 3-dimensional geometry of the heart superimposed with colour-coded electric potential maps to guide ablation.
EnSite System (manufactured by Endocardial Solutions Inc., MN) includes a multi-electrode non-contact catheter that conducts simultaneous mapping. A processing unit uses the electrical data to computes more than 3,000 isopotential electrograms that are displayed on a reconstructed 3-dimensional geometry of the heart chamber. The navigational system, EnSite NavX, can be used separately with most mapping catheters.
The LocaLisa Intracardiac System (manufactured by Medtronics Inc, MN) is a navigational system that uses an electrical field to locate the mapping catheter. It reconstructs the location of the electrodes on the mapping catheter in 3-dimensional virtual space, thereby enabling an ablation catheter to be directed to the electrode that identifies abnormal electric potential.
Polar Constellation Advanced Mapping Catheter System (manufactured by Boston Scientific, MA) is a multielectrode basket catheter with 64 electrodes on 8 splines. Once deployed, each electrode is automatically traced. The information enables a 3-dimensional model of the basket catheter to be computed. Colour-coded activation maps are reconstructed online and displayed on a monitor. By using this catheter, a precise electrical map of the atrium can be obtained in several heartbeats.
Review Strategy
A systematic search of Cochrane, MEDLINE and EMBASE was conducted to identify studies that compared ablation guided by any of the advanced systems to fluoroscopy-guided ablation of tachycardia. English-language studies with sample sizes greater than or equal to 20 that were published between 2000 and 2005 were included. Observational studies on safety of advanced mapping systems and fluoroscopy were also included. Outcomes of interest were acute success, defined as termination of arrhythmia immediately following ablation; long-term success, defined as being arrhythmia free at follow-up; total procedure time; fluoroscopy time; radiation dose; number of radiofrequency pulses; complications; cost; and the cost-effectiveness ratio.
Quality of the individual studies was assessed using established criteria. Quality of the overall evidence was determined by applying the GRADE evaluation system. (3) Qualitative synthesis of the data was performed. Quantitative analysis using Revman 4.2 was performed when appropriate.
Quality of the Studies
Thirty-four studies met the inclusion criteria. These comprised 18 studies on CARTO (4 randomized controlled trials [RCTs] and 14 non-RCTs), 3 RCTs on EnSite NavX, 4 studies on LocaLisa Navigational System (1 RCT and 3 non-RCTs), 2 studies on EnSite and CARTO, 1 on Polar Constellation basket catheter, and 7 studies on radiation safety.
The quality of the studies ranged from moderate to low. Most of the studies had small sample sizes with selection bias, and there was no blinding of patients or care providers in any of the studies. Duration of follow-up ranged from 6 weeks to 29 months, with most having at least 6 months of follow-up. There was heterogeneity with respect to the approach to ablation, definition of success, and drug management before and after the ablation procedure.
Summary of Findings
Evidence is based on a small number of small RCTS and non-RCTS with methodological flaws.
Advanced nonfluoroscopy mapping/navigation systems provided real time 3-dimensional images with integration of anatomic and electrical potential information that enable better visualization of areas of interest for ablation
Advanced nonfluoroscopy mapping/navigation systems appear to be safe; they consistently shortened the fluoroscopy duration and radiation exposure.
Evidence suggests that nonfluoroscopy mapping and navigation systems may be used as adjuncts to rather than replacements for fluoroscopy in guiding the ablation of complex arrhythmias.
Most studies showed a nonsignificant trend toward lower overall failure rate for advanced mapping-guided ablation compared with fluoroscopy-guided mapping.
Pooled analyses of small RCTs and non-RCTs that compared fluoroscopy- with nonfluoroscopy-guided ablation of atrial fibrillation and atrial flutter showed that advanced nonfluoroscopy mapping and navigational systems:
Yielded acute success rates of 69% to 100%, not significantly different from fluoroscopy ablation.
Had overall failure rates at 3 months to 19 months of 1% to 40% (median 25%).
Resulted in a 10% relative reduction in overall failure rate for advanced mapping guided-ablation compared to fluoroscopy guided ablation for the treatment of atrial fibrillation.
Yielded added benefit over fluoroscopy in guiding the ablation of complex arrhythmia. The advanced systems were shown to reduce the arrhythmia burden and the need for antiarrhythmic drugs in patients with complex arrhythmia who had failed fluoroscopy-guided ablation
Based on predominantly observational studies, circumferential PV ablation guided by a nonfluoroscopy system was shown to do the following:
Result in freedom from atrial fibrillation (with or without antiarrhythmic drug) in 75% to 95% of patients (median 79%). This effect was maintained up to 28 months.
Result in freedom from atrial fibrillation without antiarrhythmic drugs in 47% to 95% of patients (median 63%).
Improve patient survival at 28 months after the procedure as compared with drug therapy.
Require special skills; patient outcomes are operator dependent, and there is a significant learning curve effect.
Complication rates of pulmonary vein ablation guided by an advanced mapping/navigation system ranged from 0% to 10% with a median of 6% during a follow-up period of 6 months to 29 months.
The complication rate of the study with the longest follow-up was 8%.
The most common complications of advanced catheter-guided ablation were stroke, transient ischemic attack, cardiac tamponade, myocardial infarction, atrial flutter, congestive heart failure, and pulmonary vein stenosis. A small number of cases with fatal atrial-esophageal fistula had been reported and were attributed to the high radiofrequency energy used rather than to the advanced mapping systems.
Economic Analysis
An Ontario-based economic analysis suggests that the cumulative incremental upfront costs of catheter ablation of atrial fibrillation guided by advanced nonfluoroscopy mapping could be recouped in 4.7 years through cost avoidance arising from less need for antiarrhythmic drugs and fewer hospitalization for stroke and heart failure.
Expert Opinion
Expert consultants to the Medical Advisory Secretariat noted the following:
Nonfluoroscopy mapping is not necessary for simple ablation procedures (e.g., typical flutter). However, it is essential in the ablation of complex arrhythmias including these:
Symptomatic, drug-refractory atrial fibrillation
Arrhythmias in people who have had surgery for congenital heart disease (e.g., macro re-entrant tachycardia in people who have had surgery for congenital heart disease).
Ventricular tachycardia due to myocardial infarction
Atypical atrial flutter
Advanced mapping systems represent an enabling technology in the ablation of complex arrhythmias. The ablation of these complex cases would not have been feasible or advisable with fluoroscopy-guided ablation and, therefore, comparative studies would not be feasible or ethical in such cases.
Many of the studies included patients with relatively simple arrhythmias (e.g., typical atrial flutter and atrial ventricular nodal re-entrant tachycardia), for which the success rates using the fluoroscopy approach were extremely high and unlikely to be improved upon using nonfluoroscopic mapping.
By age 50, almost 100% of people who have had surgery for congenital heart disease will develop arrhythmia.
Some centres are under greater pressure because of expertise in complex ablation procedures for subsets of patients.
The use of advanced mapping systems requires the support of additional electrophysiologic laboratory time and nursing time.
For patients suffering from symptomatic, drug-refractory atrial fibrillation and are otherwise healthy, catheter ablation offers a treatment option that is less invasive than is open surgical ablation.
Small RCTs that may have been limited by type 2 errors showed significant reductions in fluoroscopy exposure in nonfluoroscopy-guided ablation and a trend toward lower overall failure rate that did not reach statistical significance.
Pooled analysis suggests that advanced mapping systems may reduce the overall failure rate in the ablation of atrial fibrillation.
Observational studies suggest that ablation guided by complex mapping/navigation systems is a promising treatment for complex arrhythmias such as highly symptomatic, drug-refractory atrial fibrillation for which rate control is not an option
In people with atrial fibrillation, ablation guided by advanced nonfluoroscopy mapping resulted in arrhythmia free rates of 80% or higher, reduced mortality, and better quality of life at experienced centres.
Although generally safe, serious complications such as stroke, atrial-esophageal, and pulmonary vein stenosis had been reported following ablation procedures.
Experts advised that advanced mapping systems are also required for catheter ablation of:
Hemodynamically unstable ventricular tachycardia from ischemic heart disease
Macro re-entrant atrial tachycardia after surgical correction of congenital heart disease
Atypical atrial flutter
Catheter ablation of atrial fibrillation is still evolving, and it appears that different ablative techniques may be appropriate depending on the characteristics of the patient and the atrial fibrillation.
Data from centres that perform electrophysiological mapping suggest that patients with drug-refractory atrial fibrillation may be the largest group with unmet need for advanced mapping-guided catheter ablation in Ontario.
Nonfluoroscopy mapping-guided pulmonary vein ablation for the treatment of atrial fibrillation has a significant learning effect; therefore, it is advisable for the province to establish centres of excellence to ensure a critical volume, to gain efficiency and to minimize the need for antiarrhythmic drugs after ablation and the need for future repeat ablation procedures.
PMCID: PMC3379531  PMID: 23074499
21.  Improving the large scale purification of the HIV microbicide, griffithsin 
BMC Biotechnology  2015;15(1):12.
Griffithsin is a broad spectrum antiviral lectin that inhibits viral entry and maturation processes through binding clusters of oligomannose glycans on viral envelope glycoproteins. An efficient, scaleable manufacturing process for griffithsin active pharmaceutical ingredient (API) is essential for particularly cost-sensitive products such as griffithsin -based topical microbicides for HIV-1 prevention in resource poor settings. Our previously published purification method used ceramic filtration followed by two chromatography steps, resulting in a protein recovery of 30%. Our objective was to develop a scalable purification method for griffithsin expressed in Nicotiana benthamiana plants that would increase yield, reduce production costs, and simplify manufacturing techniques. Considering the future need to transfer griffithsin manufacturing technology to resource poor areas, we chose to focus modifying the purification process, paying particular attention to introducing simple, low-cost, and scalable procedures such as use of temperature, pH, ion concentration, and filtration to enhance product recovery.
We achieved >99% pure griffithsin API by generating the initial green juice extract in pH 4 buffer, heating the extract to 55°C, incubating overnight with a bentonite MgCl2 mixture, and final purification with Capto™ multimodal chromatography. Griffithsin extracted with this protocol maintains activity comparable to griffithsin purified by the previously published method and we are able to recover a substantially higher yield: 88 ± 5% of griffithsin from the initial extract. The method was scaled to produce gram quantities of griffithsin with high yields, low endotoxin levels, and low purification costs maintained.
The methodology developed to purify griffithsin introduces and develops multiple tools for purification of recombinant proteins from plants at an industrial scale. These tools allow for robust cost-effective production and purification of griffithsin. The methodology can be readily scaled to the bench top or industry and process components can be used for purification of additional proteins based on biophysical characteristics.
PMCID: PMC4349730  PMID: 25887919
Griffithsin; Tobacco mosaic virus; Protein purification; N. benthamiana; Bentonite; Microbicide; HIV
22.  Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway 
PLoS Biology  2012;10(2):e1001269.
Most organisms are simply diamagnetic, while magnetotactic bacteria and migratory animals are among organisms that exploit magnetism. Biogenic magnetization not only is of fundamental interest, but also has industrial potential. However, the key factor(s) that enable biogenic magnetization in coordination with other cellular functions and metabolism remain unknown. To address the requirements for induction and the application of synthetic bio-magnetism, we explored the creation of magnetism in a simple model organism. Cell magnetization was first observed by attraction towards a magnet when normally diamagnetic yeast Saccharomyces cerevisiae were grown with ferric citrate. The magnetization was further enhanced by genetic modification of iron homeostasis and introduction of ferritin. The acquired magnetizable properties enabled the cells to be attracted to a magnet, and be trapped by a magnetic column. Superconducting quantum interference device (SQUID) magnetometry confirmed and quantitatively characterized the acquired paramagnetism. Electron microscopy and energy-dispersive X-ray spectroscopy showed electron-dense iron-containing aggregates within the magnetized cells. Magnetization-based screening of gene knockouts identified Tco89p, a component of TORC1 (Target of rapamycin complex 1), as important for magnetization; loss of TCO89 and treatment with rapamycin reduced magnetization in a TCO89-dependent manner. The TCO89 expression level positively correlated with magnetization, enabling inducible magnetization. Several carbon metabolism genes were also shown to affect magnetization. Redox mediators indicated that TCO89 alters the intracellular redox to an oxidized state in a dose-dependent manner. Taken together, we demonstrated that synthetic induction of magnetization is possible and that the key factors are local redox control through carbon metabolism and iron supply.
Author Summary
Most organisms do not respond to magnetic fields. However, “magnetotactic” bacteria and migratory animals can sense geomagnetic fields and alter their behavior accordingly. These organisms often contain small magnetic particles that may be responsible for sensing magnetic fields. In magnetotactic bacteria, specific genes are crucial for the formation of these magnetic particles, but no such genes have yet been characterized in migratory animals. In humans, formation of magnetic particles can be observed in the neuronal tissue in neurodegenerative diseases. One explanation for the appearance of these magnetic particles is that they are the result of alterations in metabolism, which occur in neurodegenerative diseases. Here, we explore this hypothesis by inducing magnetism in yeast cells, which are not naturally magnetic and examine how changes in metabolism contribute to particle formation and magnetism. We find that yeast cells expressing a set of human proteins that sequester iron contain iron particles and become attracted by a magnet when grown with ferric citrate. Through physiological and genetic studies we show that target of rapamycin complex 1 (TORC1) signaling, which responds to nutritional signals, is important for the magnetization of these cells by altering the intracellular oxidation (or redox) state. We also show that genes involved in carbon metabolism affect magnetization. We propose that local redox control mediated by carbon metabolism and iron homeostasis, processes that exist in normal unmagnetized cells, are key for iron particle formation and magnetization. We conclude that magnetization of normal cells will be possible with these existing gene sets.
PMCID: PMC3289596  PMID: 22389629
23.  Counter-current chromatography for the separation of terpenoids: a comprehensive review with respect to the solvent systems employed 
Phytochemistry Reviews  2014;13(2):547-572.
Natural products extracts are commonly highly complex mixtures of active compounds and consequently their purification becomes a particularly challenging task. The development of a purification protocol to extract a single active component from the many hundreds that are often present in the mixture is something that can take months or even years to achieve, thus it is important for the natural product chemist to have, at their disposal, a broad range of diverse purification techniques. Counter-current chromatography (CCC) is one such separation technique utilising two immiscible phases, one as the stationary phase (retained in a spinning coil by centrifugal forces) and the second as the mobile phase. The method benefits from a number of advantages when compared with the more traditional liquid–solid separation methods, such as no irreversible adsorption, total recovery of the injected sample, minimal tailing of peaks, low risk of sample denaturation, the ability to accept particulates, and a low solvent consumption. The selection of an appropriate two-phase solvent system is critical to the running of CCC since this is both the mobile and the stationary phase of the system. However, this is also by far the most time consuming aspect of the technique and the one that most inhibits its general take-up. In recent years, numerous natural product purifications have been published using CCC from almost every country across the globe. Many of these papers are devoted to terpenoids—one of the most diverse groups. Naturally occurring terpenoids provide opportunities to discover new drugs but many of them are available at very low levels in nature and a huge number of them still remain unexplored. The collective knowledge on performing successful CCC separations of terpenoids has been gathered and reviewed by the authors, in order to create a comprehensive document that will be of great assistance in performing future purifications.
PMCID: PMC4032468  PMID: 24899873
Counter-current chromatography; Terpenoids; Terpenes; Natural products; Separation; Purification
24.  Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses 
Recently, structural and biochemical studies have detailed many of the molecular events that occur in the ribosome during inhibition of protein synthesis by antibiotics and during nascent polypeptide synthesis. Some of these antibiotics, and regulatory nascent polypeptides mostly in the form of peptidyl-tRNAs, inhibit either peptide bond formation or translation termination1-7. These inhibitory events can stop the movement of the ribosome, a phenomenon termed "translational arrest". Translation arrest induced by either an antibiotic or a nascent polypeptide has been shown to regulate the expression of genes involved in diverse cellular functions such as cell growth, antibiotic resistance, protein translocation and cell metabolism8-13. Knowledge of how antibiotics and regulatory nascent polypeptides alter ribosome function is essential if we are to understand the complete role of the ribosome in translation, in every organism.
Here, we describe a simple methodology that can be used to purify, exclusively, for analysis, those ribosomes translating a specific mRNA and containing a specific peptidyl-tRNA14. This procedure is based on selective isolation of translating ribosomes bound to a biotin-labeled mRNA. These translational complexes are separated from other ribosomes in the same mixture, using streptavidin paramagnetic beads (SMB) and a magnetic field (MF). Biotin-labeled mRNAs are synthesized by run-off transcription assays using as templates PCR-generated DNA fragments that contain T7 transcriptional promoters. T7 RNA polymerase incorporates biotin-16-UMP from biotin-UTP; under our conditions approximately ten biotin-16-UMP molecules are incorporated in a 600 nt mRNA with a 25% UMP content. These biotin-labeled mRNAs are then isolated, and used in in vitro translation assays performed with release factor 2 (RF2)-depleted cell-free extracts obtained from Escherichia coli strains containing wild type or mutant ribosomes. Ribosomes translating the biotin-labeled mRNA sequences are stalled at the stop codon region, due to the absence of the RF2 protein, which normally accomplishes translation termination. Stalled ribosomes containing the newly synthesized peptidyl-tRNA are isolated and removed from the translation reactions using SMB and an MF. These beads only bind biotin-containing messages.
The isolated, translational complexes, can be used to analyze the structural and functional features of wild type or mutant ribosomal components, or peptidyl-tRNA sequences, as well as determining ribosome interaction with antibiotics or other molecular factors 1,14-16. To examine the function of these isolated ribosome complexes, peptidyl-transferase assays can be performed in the presence of the antibiotic puromycin1. To study structural changes in translational complexes, well established procedures can be used, such as i) crosslinking to specific amino acids14 and/or ii) alkylation protection assays1,14,17.
PMCID: PMC3197406  PMID: 21403627
25.  Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures 
BMC Genomics  2012;13:105.
Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself.
Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T), intermediate g* (0.1 g* at B = 14.7 T) and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T) plus an internal 1 g* control (B = 16.5 T). The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg) and a Large Diameter Centrifuge (2 g).
Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies.
A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR). A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment.
PMCID: PMC3368779  PMID: 22435851

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