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1.  Ethanol effect on metabolic activity of the ethalogenic fungus Fusarium oxysporum 
BMC Biotechnology  2015;15:15.
Background
Fusarium oxysporum is a filamentous fungus which has attracted a lot of scientific interest not only due to its ability to produce a variety of lignocellulolytic enzymes, but also because it is able to ferment both hexoses and pentoses to ethanol. Although this fungus has been studied a lot as a cell factory, regarding applications for the production of bioethanol and other high added value products, no systematic study has been performed concerning its ethanol tolerance levels.
Results
In aerobic conditions it was shown that both the biomass production and the specific growth rate were affected by the presence of ethanol. The maximum allowable ethanol concentration, above which cells could not grow, was predicted to be 72 g/L. Under limited aeration conditions the ethanol-producing capability of the cells was completely inhibited at 50 g/L ethanol. The lignocellulolytic enzymatic activities were affected to a lesser extent by the presence of ethanol, while the ethanol inhibitory effect appears to be more severe at elevated temperatures. Moreover, when the produced ethanol was partially removed from the broth, it led to an increase in fermenting ability of the fungus up to 22.5%. The addition of F. oxysporum’s system was shown to increase the fermentation of pretreated wheat straw by 11%, in co-fermentation with Saccharomyces cerevisiae.
Conclusions
The assessment of ethanol tolerance levels of F. oxysporum on aerobic growth, on lignocellulolytic activities and on fermentative performance confirmed its biotechnological potential for the production of bioethanol. The cellulolytic and xylanolytic enzymes of this fungus could be exploited within the biorefinery concept as their ethanol resistance is similar to that of the commercial enzymes broadly used in large scale fermentations and therefore, may substantially contribute to a rational design of a bioconversion process involving F. oxysporum. The SSCF experiments on liquefied wheat straw rich in hemicellulose indicated that the contribution of the metabolic system of F. oxysporum in a co-fermentation with S. cerevisiae may play a secondary role.
doi:10.1186/s12896-015-0130-3
PMCID: PMC4417268  PMID: 25887038
Bioethanol; Ethanol inhibition; Ethanol tolerance; Ethanol removal; Fusarium oxysporum
2.  High-level expression of human arginase I in Pichia pastoris and its immobilization on chitosan to produce L-ornithine 
BMC Biotechnology  2015;15:66.
Background
L-ornithine (L-Orn), is an intermediate metabolite in the urea cycle that plays a significant role in humans. L-Orn can be obtained from the catalysis of L-arginine (L-Arg) by arginase. The Pichia pastoris expression system offers the possibility of generating a large amount of recombinant protein. The immobilized enzyme technology can overcome the difficulties in recovery, recycling and long-term stability that result from the use of free enzyme.
Methods
The recombinant human arginase I (ARG I) was obtained using an optimized method with the Pichia pastoris GS115 as the host strain. Chitosan paticles were cross-linked with glutaraldehyde and rinsed exhaustively. Then the expressed ARG I was immobilized on the crosslinked chitosan particles, and the enzymatic properties of both the free and immobilized enzymes were evaluated. At last, the immobilized ARG I was employed to catalyze L-Arg to L-Orn.
Results
The results indicated that these two states both exhibited optimal activity under the same condition of pH10 at 40 °C. However, the immobilized ARG I exhibited the remarkable thermal and long-term stability as well as broad adaptability to pH, suggesting its potential for wide application in future industry. After a careful analysis of its catalytic conditions, immobilized ARG I was employed to catalyze the conversion of L-Arg to L-Orn under optimal condition of 1 % glutaraldehyde, 1 mM Mn2+, 40 °C, pH10 and an L-arginine (L-Arg) concentration of 200 g/L, achieving a highly converted content of 149.g/L L-Orn.
Conclusions
In this work, ARG Ι was abundantly expressed, and an efficient, facile and repeatable method was developed to synthesize high-quality L-Orn. This method not only solved the problem of obtaining a large amount of arginase, but also provided a promising alternative for the future industrial production of L-Orn.
doi:10.1186/s12896-015-0184-2
PMCID: PMC4521451  PMID: 26227111
L-ornithine; Recombinant human arginase I; Immobilization; Chitosan; L-arginine; Transformation
3.  Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq 
BMC Biotechnology  2015;15:65.
Background
RNA-Seq has enabled high-throughput gene expression profiling to provide insight into the functional link between genotype and phenotype. Low quantities of starting RNA can be a severe hindrance for studies that aim to utilize RNA-Seq. To mitigate this bottleneck, whole transcriptome amplification (WTA) technologies have been developed to generate sufficient sequencing targets from minute amounts of RNA. Successful WTA requires accurate replication of transcript abundance without the loss or distortion of specific mRNAs. Here, we test the efficacy of NuGEN’s Ovation RNA-Seq V2 system, which uses linear isothermal amplification with a unique chimeric primer for amplification, using white adipose tissue from standard laboratory rats (Rattus norvegicus). Our goal was to investigate potential biological artifacts introduced through WTA approaches by establishing comparisons between matched raw and amplified RNA libraries derived from biological replicates.
Results
We found that 93% of expressed genes were identical between all unamplified versus matched amplified comparisons, also finding that gene density is similar across all comparisons. Our sequencing experiment and downstream bioinformatic analyses using the Tuxedo analysis pipeline resulted in the assembly of 25,543 high-quality transcripts. Libraries constructed from raw RNA and WTA samples averaged 15,298 and 15,253 expressed genes, respectively. Although significant differentially expressed genes (P < 0.05) were identified in all matched samples, each of these represents less than 0.15% of all shared genes for each comparison.
Conclusions
Transcriptome amplification is efficient at maintaining relative transcript frequencies with no significant bias when using this NuGEN linear isothermal amplification kit under ideal laboratory conditions as presented in this study. This methodology has broad applications, from clinical and diagnostic, to field-based studies when sample acquisition, or sample preservation, methods prove challenging.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0155-7) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0155-7
PMCID: PMC4520150
RNA-Seq; Whole transcriptome amplification; White adipose tissue; Rattus norvegicus
4.  Expression of dsRNA in recombinant Isaria fumosorosea strain targets the TLR7 gene in Bemisia tabaci 
BMC Biotechnology  2015;15:64.
Background
RNA interference (RNAi) technology shows a great potential in controlling agricultural pests, despite the difficulty of introducing exogenous dsRNA/siRNA into target pests. Isaria fumosorosea is a common fungal pathogen of the B-biotype Bemisia tabaci (whitefly), which is a widespread pest. Entomopathogenic fungi directly penetrate the cuticle and invade insect hemocoel. Application of I. fumosorosea expressing dsRNA of whitefly immunity-related gene may aid in developing RNAi technology to effectively control whiteflies.
Methods
A dsRNA expression plasmid, psTLR7, was constructed by introducing the Toll-like receptor 7 (TLR7) gene of B-biotype whitefly to the silent vector, pSilent-1. The plasmid psTLR7 was transferred into the protoplast of the I. fumosorosea strain IfB01. Then, the recombinant strain was screened out based on the biological stability and bioactivity against whitefly.
Results
A genetically stable recombinant strain IfB01-TRL7 was screened out. The impact of IfB01-TRL7 against whitefly TRL7 gene was validated by qPCR. Lower expression levels of the TLR7 gene was observed in the whiteflies infected by the recombinant strain. The bioassay results indicated that compared to IfB01 strain, IfB01-TRL7 increased the mortality of whitefly nymphs, and decreased and shortened the values of LC50 and LT50, thus indicating higher virulence of IfB01-TRL7.
Conclusion
The expression of the dsRNA of whitefly TLR7 gene in recombinant I. fumosorosea strain successfully knocked down the host target gene by infecting the nymphs and enhanced the whiteflies mortality. The present study will give insight to new application of RNAi technology for more effective biocontrol of this pests.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0170-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0170-8
PMCID: PMC4509747  PMID: 26198409
Isaria fumosorosea; Recombinant strain; dsRNA; Whitefly
5.  Natural phenolics greatly increase flax (Linum usitatissimum) oil stability 
BMC Biotechnology  2015;15:62.
Background
Flaxseed oil is characterized by high content of essential polyunsaturated fatty acids (PUFA) promoted as a human dietary supplement protecting against atherosclerosis. The disadvantage of the high PUFA content in flax oil is high susceptibility to oxidation, which can result in carcinogenic compound formation. Linola flax cultivar is characterized by high linoleic acid content in comparison to traditional flax cultivars rich in linolenic acid. The changes in fatty acid proportions increase oxidative stability of Linola oil and broaden its use as an edible oil for cooking. However one of investigated transgenic lines has high ALA content making it suitable as omega-3 source. Protection of PUFA oxidation is a critical factor in oil quality. The aim of this study was to investigate the impact of phenylpropanoid contents on the oil properties important during the whole technological process from seed storage to grinding and oil pressing, which may influence health benefits as well as shelf-life, and to establish guidelines for the selection of new cultivars.
Methods
The composition of oils was determined by chromatographic (GS-FID and LC-PDA-MS) methods. Antioxidant properties of secondary metabolites were analyzed by DPPH method. The stability of oils was investigated: a) during regular storage by measuring acid value peroxide value p-anisidine value malondialdehyde, conjugated dienes and trienes; b) by using accelerated rancidity tests by TBARS reaction; c) by thermoanalytical - differential scanning calorimetry (DSC).
Results
In one approach, in order to increase oil stability, exogenous substances added are mainly lipid soluble antioxidants from the isoprenoid pathway, such as tocopherol and carotene. The other approach is based on transgenic plant generation that accumulates water soluble compounds. Increased accumulation of phenolic compounds in flax seeds was achieved by three different strategies that modify genes coding for enzymes from the phenylpropanoid pathway. The three types of transgenic flax had different phenylpropanoid profiles detected in oil, highly increasing its stability.
Conclusions
We found that hydrophilic phenylpropanoids more than lipophilic isoprenoid compounds determine oil stability however they can work synergistically. Among phenolics the caffeic acid was most effective in increasing oil stability.
doi:10.1186/s12896-015-0178-0
PMCID: PMC4485345  PMID: 26123633
Flaxseed oil; Oil stability; Antioxidant activity; Phenolic compounds; Radical scavenging activity
6.  Heterologous expression of flax PHOSPHOLIPID:DIACYLGLYCEROL CHOLINEPHOSPHOTRANSFERASE (PDCT) increases polyunsaturated fatty acid content in yeast and Arabidopsis seeds 
BMC Biotechnology  2015;15:63.
Background
Flax (Linum usitatissimum L.) is an agriculturally important crop with seed oil enriched in α-linolenic acid (18:3 cisΔ9, 12, 15; ALA). This polyunsaturated fatty acid (PUFA) is the major determinant for the quality of flax seed oil in food, nutraceuticals and industrial applications. The recently identified enzyme: phosphatidylcholine diacylglycerol cholinephosphotransferase (PDCT), catalyzes the interconversion between phosphatidylcholine (PC) and diacylglycerol (DAG), and has been shown to play an important role in PUFA accumulation in Arabidopsis thaliana seeds.
Methods
Two flax PDCT genes were identified using homology-based approach.
Results
In this study, we describe the isolation and characterization of two PDCT genes from flax (LuPDCT1 and LuPDCT2) with very high nucleotide sequence identity (97%) whose deduced amino acid sequences exhibited approximately 55% identity with that of A. thaliana PDCT (AtROD1). The genes encoded functionally active enzymes that were strongly expressed in developing embryos. Complementation studies with the A. thaliana rod1 mutant demonstrated that the flax PDCTs were capable of restoring PUFA levels in planta. Furthermore, PUFA levels increased in Saccharomyces cerevisiae when the flax PDCTs were co-expressed with FATTY ACID DESATURASES (FADs), FAD2 and FAD3, while seed-specific expression of LuPDCT1 and LuPDCT2 in A. thaliana resulted in 16.4% and 19.7% increases in C18-PUFAs, respectively, with a concomitant decrease in the proportion of oleic acid (18:1cisΔ9; OA).
Conclusions
The two novel PDCT homologs from flax are capable of increasing C18-PUFA levels substantially in metabolically engineered yeast and transgenic A. thaliana seeds. These flax PDCT proteins appear to play an important dual role in the determination of PUFA content by efficiently channelling monounsaturated FAs into PC for desaturation and moving the resulting PUFAs out of PC for subsequent use in TAG synthesis. These results indicate that flax PDCTs would be useful for bioengineering of oil crops to increase PUFA levels for applications in human food and nutritional supplements, animal feed and industrial bioproducts.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0156-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0156-6
PMCID: PMC4486708  PMID: 26123542
α-linolenic acid; Linum usitatissimum; Phosphatidylcholine-diacyglycerol interconversion; AtROD1; PUFA; Saccharomyces cerevisiae
7.  Secretion of Fc-amidated peptide fusion proteins by Chinese hamster ovary cells 
BMC Biotechnology  2015;15:61.
Background
The therapeutic use of α-amidated peptides (e.g. calcitonin, glucagon-like peptide) has increased dramatically, but there are major impediments to wider use of such peptides. Larger peptides are expensive to synthesize, and short plasma half-lives frequently limit the clinical circumstances in which the peptides would be useful. Both problems are potentially solved by producing peptides as fusions with the Fc region of human immunoglobulin.
Methods
Glucagon-like peptide 1 (GLP1), peptide YY (PYY) and neuromedin U (NMU) were expressed and purified from stable CHO lines; since the α-amide group is essential for full biological potency of many peptides, Fc-fusion peptides were expressed in CHO lines stably expressing the α-amidating enzyme, peptidylglycine α-amidating monooxygenase (PAM: EC 1.14.17.3). Purified fusion proteins were analyzed intact and after HRV3C rhinovirus protease cleavage, at a site in the linker separating the Fc region from the peptide, by mass spectrometry and amide-specific immunoassays.
Results
The Fc fusions were expressed at 1–2.5 μg/mg cell protein and secreted at 5-20 % of cell content per hour, in a peptide-specific manner. CHO cells express measurable endogenous PAM activity, amidating 25 % of Fc-PYY and almost 90 % of Fc-GLP1. Expression of exogenous PAM increased the level of peptide amidation to 50 % of Fc-PYY and 95 % of Fc-NMU. The Fc-GLP1 fusions were 10,000-fold less active than synthetic GLP1 in a cell-receptor cyclic AMP-based assay, as expected since the amino terminal of GLP1 is essential for full biological activity. The Fc-PYY fusions were 100-fold less active than PYY-NH2 but 10-fold more active than non-amidated PYY-Gly.
Conclusions
This type of approach can be used for the production of stabilized α-amidated peptides aimed at clinical trials.
doi:10.1186/s12896-015-0173-5
PMCID: PMC4482046  PMID: 26116580
Amidation; CHO cells; Mass spectrometry; Glucagon-like peptide 1; Peptide YY; Neuromedin U
8.  SH2-PLA: a sensitive in-solution approach for quantification of modular domain binding by proximity ligation and real-time PCR 
BMC Biotechnology  2015;15:60.
Background
There is a great interest in studying phosphotyrosine dependent protein-protein interactions in tyrosine kinase pathways that play a critical role in many aspects of cellular function. We previously established SH2 profiling, a phosphoproteomic approach based on membrane binding assays that utilizes purified Src Homology 2 (SH2) domains as a molecular tool to profile the global tyrosine phosphorylation state of cells. However, in order to use this method to investigate SH2 binding sites on a specific target in cell lysate, additional procedures such as pull-down or immunoprecipitation which consume large amounts of sample are required.
Results
We have developed PLA-SH2, an alternative in-solution modular domain binding assay that takes advantage of Proximity Ligation Assay and real-time PCR. The SH2-PLA assay utilizes oligonucleotide-conjugated anti-GST and anti-EGFR antibodies recognizing a GST-SH2 probe and cellular EGFR, respectively. If the GST-SH2 and EGFR are in close proximity as a result of SH2-phosphotyrosine interactions, the two oligonucleotides are brought within a suitable distance for ligation to occur, allowing for efficient complex amplification via real-time PCR. The assay detected signal across at least 3 orders of magnitude of lysate input with a linear range spanning 1–2 orders and a low femtomole limit of detection for EGFR phosphotyrosine. SH2 binding kinetics determined by PLA-SH2 showed good agreement with established far-Western analyses for A431 and Cos1 cells stimulated with EGF at various times and doses. Further, we showed that PLA-SH2 can survey lung cancer tissues using 1 μl lysate without requiring phospho-enrichment.
Conclusions
We showed for the first time that interactions between SH2 domain probes and EGFR in cell lysate can be determined in a microliter-scale assay using SH2-PLA. The obvious benefit of this method is that the low sample requirement allows detection of SH2 binding in samples which are difficult to analyze using traditional protein interaction assays. This feature along with short assay runtime makes this method a useful platform for the development of high throughput assays to determine modular domain–ligand interactions which could have wide-ranging applications in both basic and translational cancer research.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0169-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0169-1
PMCID: PMC4482279  PMID: 26112401
SH2; Proximity ligation; SH2-PLA; Modular protein domains; EGFR signaling
9.  A delivery system for field application of paratransgenic control 
BMC Biotechnology  2015;15:59.
Background
As an alternative to chemical pesticides, paratransgenesis relies on transformation of symbiotic bacteria of an arthropod vector to deliver molecules that disrupt pathogen transmission. For over a decade paratransgenesis has remained a laboratory-based endeavor owing to regulatory concerns regarding introduction of transformed microorganisms into the environment. To facilitate field application of paratransgenic strategies, risk mitigation approaches that address environmental contamination and gene spread must be developed.
Results
Using biopolymer manipulation, we introduce a novel microencapsulation platform for containment and targeted delivery of engineered bacteria to the gut of a disease-transmitting arthropod. We demonstrate the first proof of principle of targeted delivery of EPA-approved Pantoea agglomerans E325 in a paratransgenic system to control spread of Pierce’s Disease by glassy-winged sharpshooters, (Homalodisca vitripennis) under simulated field conditions. Engineered microcapsules may address regulatory concerns regarding containment of recombinant bacteria and environmental spread of foreign genetic material and may represent an important step in translating paratransgenic science beyond the lab and into the field.
Conclusions
We present, for the first time, a microencapsulation strategy to deliver recombinant bacteria to an insect and demonstrate targeted release of bacteria into the physiologically relevant region of the insect gut. This is a first step toward addressing concerns related to field application of recombinant bacteria. Engineered microparticles may decrease environmental contamination, horizontal gene transfer and competition with native species by acting as a barrier between recombinant bacteria and the environment.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0175-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0175-3
PMCID: PMC4477610  PMID: 26099939
Paratransgenesis; Microencapsulation; Pierce’s Disease; Xylella fastidiosa; Homalodisca vitripennis; Pantoea agglomerans; Calcium-alginate
10.  Retargeting of microcell fusion towards recipient cell-oriented transfer of human artificial chromosome 
BMC Biotechnology  2015;15:58.
Background
Human artificial chromosome (HAC) vectors have some unique characteristics as compared with conventional vectors, carrying large transgenes without size limitation, showing persistent expression of transgenes, and existing independently from host genome in cells. With these features, HACs are expected to be promising vectors for modifications of a variety of cell types. However, the method of introduction of HACs into target cells is confined to microcell-mediated chromosome transfer (MMCT), which is less efficient than other methods of vector introduction. Application of Measles Virus (MV) fusogenic proteins to MMCT instead of polyethylene glycol (PEG) has partly solved this drawback, whereas the tropism of MV fusogenic proteins is restricted to human CD46- or SLAM-positive cells.
Results
Here, we show that retargeting of microcell fusion by adding anti-Transferrin receptor (TfR) single chain antibodies (scFvs) to the extracellular C-terminus of the MV-H protein improves the efficiency of MV-MMCT to human fibroblasts which originally barely express both native MV receptors, and are therefore resistant to MV-MMCT. Efficacy of chimeric fusogenic proteins was evaluated by the evidence that the HAC, tagged with a drug-resistant gene and an EGFP gene, was transferred from CHO donor cells into human fibroblasts. Furthermore, it was demonstrated that no perturbation of either the HAC status or the functions of transgenes was observed on account of retargeted MV-MMCT when another HAC carrying four reprogramming factors (iHAC) was transferred into human fibroblasts.
Conclusions
Retargeted MV-MMCT using chimeric H protein with scFvs succeeded in extending the cell spectrum for gene transfer via HAC vectors. Therefore, this technology could facilitate the systematic cell engineering by HACs.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0142-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0142-z
PMCID: PMC4472177  PMID: 26088202
Human artificial chromosome; Measles Virus fusogenic protein; Chimeric protein
11.  Active fungal GH115 α-glucuronidase produced in Arabidopsis thaliana affects only the UX1-reactive glucuronate decorations on native glucuronoxylans 
BMC Biotechnology  2015;15:56.
Background
Expressing microbial polysaccharide-modifying enzymes in plants is an attractive approach to custom tailor plant lignocellulose and to study the importance of wall structures to plant development. Expression of α-glucuronidases in plants to modify the structures of glucuronoxylans has not been yet attempted. Glycoside hydrolase (GH) family 115 α-glucuronidases cleave the internal α-D-(4-O-methyl)glucopyranosyluronic acid ((Me)GlcA) from xylans or xylooligosaccharides. In this work, a GH115 α-glucuronidase from Schizophyllum commune, ScAGU115, was expressed in Arabidopsis thaliana and targeted to apoplast. The transgene effects on native xylans’ structures, plant development, and lignocellulose saccharification were evaluated and compared to those of knocked out glucuronyltransferases AtGUX1 and AtGUX2.
Results
The ScAGU115 extracted from cell walls of Arabidopsis was active on the internally substituted aldopentaouronic acid (XUXX). The transgenic plants did not show any change in growth or in lignocellulose saccharification. The cell wall (Me)GlcA and other non-cellulosic sugars, as well as the lignin content, remained unchanged. In contrast, the gux1gux2 double mutant showed a 70% decrease in (Me)GlcA to xylose molar ratio, and, interestingly, a 60% increase in the xylose content. Whereas ScAGU115-expressing plants exhibited a decreased signal in native secondary walls from the monoclonal antibody UX1 that recognizes (Me)GlcA on non-acetylated xylan, the signal was not affected after wall deacetylation. In contrast, gux1gux2 mutant was lacking UX1 signals in both native and deacetylated cell walls. This indicates that acetyl substitution on the xylopyranosyl residue carrying (Me)GlcA or on the neighboring xylopyranosyl residues may restrict post-synthetic modification of xylans by ScAGU115 in planta.
Conclusions
Active GH115 α-glucuronidase has been produced for the first time in plants. The cell wall–targeted ScAGU115 was shown to affect those glucuronate substitutions of xylan, which are accessible to UX1 antibody and constitute a small fraction in Arabidopsis, whereas majority of (Me)GlcA substitutions were resistant, most likely due to the shielding by acetyl groups. Plants expressing ScAGU115 did not show any defects under laboratory conditions indicating that the UX1 epitope of xylan is not essential under these conditions. Moreover the removal of the UX1 xylan epitope does not affect lignocellulose saccharification.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0154-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0154-8
PMCID: PMC4472178  PMID: 26084671
Xylan acetylation; Alpha-glucuronidase; 4-O-methylglucuronic acid; Glucuronoxylan; Xylan degradation; Feedstocks for biofuels; Secondary cell walls
12.  Structural differences of amyloid-β fibrils revealed by antibodies from phage display 
BMC Biotechnology  2015;15:57.
Background
Beside neurofibrillary tangles, amyloid plaques are the major histological hallmarks of Alzheimer’s disease (AD) being composed of aggregated fibrils of β-amyloid (Aβ). During the underlying fibrillogenic pathway, starting from a surplus of soluble Aβ and leading to mature fibrils, multiple conformations of this peptide appear, including oligomers of various shapes and sizes. To further investigate the fibrillization of β-amyloid and to have tools at hand to monitor the distribution of aggregates in the brain or even act as disease modulators, it is essential to develop highly sensitive antibodies that can discriminate between diverse aggregates of Aβ.
Results
Here we report the generation and characterization of a variety of amyloid-β specific human and human-like antibodies. Distinct fractions of monomers and oligomers of various sizes were separated by size exclusion chromatography (SEC) from Aβ42 peptides. These antigens were used for the generation of two Aβ42 specific immune scFv phage display libraries from macaque (Macaca fascicularis). Screening of these libraries as well as two naïve human phage display libraries resulted in multiple unique binders specific for amyloid-β. Three of the obtained antibodies target the N-terminal part of Aβ42 although with varying epitopes, while another scFv binds to the α-helical central region of the peptide. The affinities of the antibodies to various Aβ42 aggregates as well as their ability to interfere with fibril formation and disaggregation of preformed fibrils were determined. Most significantly, one of the scFv is fibril-specific and can discriminate between two different fibril forms resulting from variations in the acidity of the milieu during fibrillogenesis.
Conclusion
We demonstrated that the approach of animal immunization and subsequent phage display based antibody selection is applicable to generate highly specific anti β-amyloid scFvs that are capable of accurately discriminating between minute conformational differences.
doi:10.1186/s12896-015-0146-8
PMCID: PMC4472244  PMID: 26084577
Alzheimer’s disease; Aβ; Abeta; Beta-amyloid; Phage display; Immune library; scFv
13.  In vivo tracking of human placenta derived mesenchymal stem cells in nude mice via14C-TdR labeling 
BMC Biotechnology  2015;15:55.
Background
In order to shed light on the regenerative mechanism of mesenchymal stem cells (MSCs) in vivo, the bio-distribution profile of implanted cells using a stable and long-term tracking method is needed. We herein investigated the bio-distribution of human placental deciduas basalis derived MSCs (termed as PDB-MSCs) in nude mice after intravenous injection by carbon radioisotope labeling thymidine (14C-TdR), which is able to incorporate into new DNA strands during cell replication.
Results
The proliferation rate and radioactive emission of human PDB-MSCs after labeled with different concentrations of 14C-TdR were measured. PDB-MSCs labeled with 1 μCi possessed high radioactivity, and the biological characteristics (i.e. morphology, colony forming ability, differentiation capabilities, karyotype and cell cycle) showed no significant changes after labeling. Thus, 1 μCi was the optimal concentration in this experimental design. In nude mice, 1 × 10614C-TdR-labeled PDB-MSCs were injected intravenously and the organs were collected at days 1, 2, 3, 5, 30 and 180 after injection, respectively. Radiolabeled PDB-MSCs were found mainly in the lung, liver, spleen, stomach and left femur of the recipient nude mice at the whole observation period.
Conclusions
This work provided solid evidence that 14C-TdR labeling did not alter the biological characteristics of human placental MSCs, and that this labeling method has potential to decrease the signal from non-infused or dead cells for cell tracking. Therefore, this labeling technique can be utilized to quantify the infused cells after long-term follow-up in pre-clinical studies.
doi:10.1186/s12896-015-0174-4
PMCID: PMC4465458  PMID: 26070459
14.  High-level expression of a novel liver-targeting fusion interferon with preferred Escherichia coli codon preference and its anti-hepatitis B virus activity in vivo 
BMC Biotechnology  2015;15:54.
Background
In our previous study, a novel liver-targeting fusion interferon (IFN-CSP) combining IFN α2b with plasmodium region I peptide was successfully constructed. IFN-CSP has significant inhibition effects on HBV-DNA replication in HepG2.2.15 cells. The aim of the present investigation was focused on how to produce high levels of recombinant IFN-CSP and its in vivo anti-hepatitis B virus (HBV) activity.
Methods
A modified DNA fragment encoding IFN-CSP was synthesized according to Escherichia coli (E. coli) preferred codon usage and transformed into E. coli BL21 (DE3) for protein expression. The induction conditions were systematically examined by combining one-factor experiments with an orthogonal test (L(9)(3)(4)). The antigenicity of the purified protein was characterized by western blot analysis. The in vivo tissue distribution were assayed and compared with native IFN α2b. HBV-transgenic mice were used as in vivo model to evaluate the anti-HBV effect of the recombinant IFN-CSP.
Results
The results showed that the E. coli expression system was very efficient to produce target protein.
Conclusion
Our current research demonstrates for the first time that IFN-CSP gene can be expressed at high levels in E. coli through codon and expression conditions optimization. The purified recombinant IFN-CSP showed liver-targeting potentiality and anti-HBV activity in vivo. The present study further supported the application of IFN-CSP in liver-targeting anti-HBV medicines.
doi:10.1186/s12896-015-0177-1
PMCID: PMC4464711  PMID: 26063245
Preferred codon usage; Induction conditions optimize; Recombinant liver-targeting fusion interferon; HBV transgenic mice
15.  Characterization of the 4,6-α-glucanotransferase GTFB enzyme of Lactobacillus reuteri 121 isolated from inclusion bodies 
BMC Biotechnology  2015;15:49.
Background
The GTFB enzyme of the probiotic bacterium Lactobacillus reuteri 121 is a 4,6-α-glucanotransferase of glycoside hydrolase family 70 (GH70; http://www.cazy.org). Contrary to the glucansucrases in GH70, GTFB is unable to use sucrose as substrate, but instead converts malto-oligosaccharides and starch into isomalto-/malto- polymers that may find application as prebiotics and dietary fibers. The GTFB enzyme expresses well in Escherichia coli BL21 Star (DE3), but mostly accumulates in inclusion bodies (IBs) which generally contain wrongly folded protein and inactive enzyme.
Methods
Denaturation followed by refolding, as well as ncIB preparation were used for isolation of active GTFB protein from inclusion bodies. Soluble, refolded and ncIB GTFB were compared using activity assays, secondary structure analysis by FT-IR, and product analyses by NMR, HPAEC and SEC.
Results
Expression of GTFB in E. coli yielded > 100 mg/l relatively pure and active but mostly insoluble GTFB protein in IBs, regardless of the expression conditions used. Following denaturing, refolding of GTFB protein was most efficient in double distilled H2O. Also, GTFB ncIBs were active, with approx. 10 % of hydrolysis activity compared to the soluble protein. When expressed as units of activity obtained per liter E. coli culture, the total amount of ncIB GTFB expressed possessed around 180 % hydrolysis activity and 100 % transferase activity compared to the amount of soluble GTFB enzyme obtained from one liter culture. The product profiles obtained for the three GTFB enzyme preparations were similar when analyzed by HPAEC and NMR. SEC investigation also showed that these 3 enzyme preparations yielded products with similar size distributions. FT-IR analysis revealed extended β-sheet formation in ncIB GTFB providing an explanation at the molecular level for reduced GTFB activity in ncIBs. The thermostability of ncIB GTFB was relatively high compared to the soluble and refolded GTFB.
Conclusion
In view of their relatively high yield, activity and high thermostability, both refolded and ncIB GTFB derived from IBs in E. coli may find industrial application in the synthesis of modified starches.
doi:10.1186/s12896-015-0163-7
PMCID: PMC4459449  PMID: 26050651
Lactobacillus reuteri; 4,6-α-glucanotransferase; GTFB enzyme; Modified starch; Dietary fiber; Inclusion bodies
16.  High-level expression, purification, and enzymatic characterization of truncated human plasminogen (Lys531-Asn791) in the methylotrophic yeast Pichia pastoris 
BMC Biotechnology  2015;15:50.
Background
Plasmin is a serine protease that plays a critical role in fibrinolysis, which is a process that prevents blood clots from growing and becoming problematic. Recombinant human microplasminogen (rhμPlg) is a derivative of plasmin that solely consists of the catalytic domain of human plasmin and lacks the five kringle domains found in the native protein. Developing an industrial production method that provides high yields of this protein with high purity, quality, and potency is critical for preclinical research.
Results
The human microplasminogen gene was cloned into the pPIC9K vector, and the recombinant plasmid was transformed into Pichia pastoris strain GS115. The concentration of plasmin reached 510.1 mg/L of culture medium. Under fermentation conditions, the yield of rhμPlg was 1.0 g/L. We purified rhμPlg to 96 % purity by gel-filtration and cation-exchange chromatography. The specific activity of rhμPlg reached 23.6 U/mg. The Km of substrate hydrolysis by recombinant human microplasmin was comparable to that of human plasmin, while rhμPlm had higher kcat/Km values than plasmin. The high purity and activity of the rhμPlg obtained here will likely prove to be a valuable tool for studies of its application in thrombotic diseases and vitreoretinopathies.
Conclusions
Reliable rhμPlg production (for use in therapeutic applications) is feasible using genetically modified P. pastoris as a host strain. The successful expression of rhμPlg in P. pastoris lays a solid foundation for its downstream application.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0179-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0179-z
PMCID: PMC4460660  PMID: 26054637
Truncated plasminogen; Plasmin; Pichia pastoris; Purification; rhμPlg
17.  Ghrelin accelerates the growth and osteogenic differentiation of rabbit mesenchymal stem cells through the ERK1/2 pathway 
BMC Biotechnology  2015;15:51.
Background
Mesenchymal stem cells (MSCs) can differentiate into chondroblasts, adipocytes, or osteoblasts under appropriate stimulation. Ghrelin, an endogenous ligand for the growth hormone secretagogue receptor (GHSR), stimulates growth hormone (GH) secretion, and has both orexigenic and adipogenic effects. This study sought to understand the potential involvement of members of MAPK serine/threonine kinases in the ghrelin-induced growth of rabbit MSCs ( rBMSC).
Methods
We applied various concentrations of ghrelin to cultured rBMSC and observed the growth rate of the cells by MTT, changes in the phosphorylation state of ERK1/2, JNK and p38, and the expression levels of ALP, Runx2, and Osterix by wetern blot.
Results
We found that the growth and osteogenic differentiation of ghrelin-treated rBMSC are promoted primarily by phosphorylated ERK1/2, and that this phosphorylation, as well p38 phosphorylation, is mediated by GHSR.
Conclusions
Our study suggests that ghrelin promotes the growth and osteogenic differentiation of rBMSC primarily through the ERK1/2 pathway.
doi:10.1186/s12896-015-0176-2
PMCID: PMC4460755  PMID: 26054524
rBMSC; MAPK; Ghrelin; Osteogenic differentiation
18.  A folded and immunogenic IgE-hyporeactive variant of the major allergen Phl p 1 produced in Escherichia coli 
BMC Biotechnology  2015;15:52.
Background
Group 1 grass pollen allergens are a major cause of allergic disease. Specific immunotherapy involving controlled administration of allergens can be used as a disease-modifying treatment for such disease. Recombinant allergen variants with reduced IgE binding capacity may be used as component in such vaccines, as they may induce fewer treatment side effects than materials currently in use. A mutated variant of the immunodominant C-terminal domain of the group 1 grass pollen allergen Phl p 1 was recently established through an approach that used a set of human monoclonal IgE as a guide to identify mutations that disturbed IgE-allergen interactions. Further analysis of this domain is required to establish its potential for use in treatment.
Methods
GST-tagged wild-type and mutated C-terminal domains of Phl p 1 were produced in Escherichia coli TUNER(DE3). The products were purified by affinity chromatography on immobilized glutathione. GST was removed by enzymatic cleavage and tag-free products were purified by size exclusion chromatography. Products were assessed by SDS-PAGE, circular dichroism spectroscopy, differential scanning fluorimetry and dynamic light scattering. Rats were immunized with GST-tagged and tag-free mutated C-terminal domain of Phl p 1. Antigen-binding properties of induced antibodies were assessed by immunochemical analysis.
Results
The mutated domain has a structure very similar to that of the wild-type domain as determined by circular dichroism, but a reduced thermal stability. Immunization of rats demonstrates that this IgE-hyporeactive domain, despite its three sequence modifications (K8A, N11A, D55A), is able to induce antibodies that substantially block the binding of allergic subjects’ IgE to the wild-type allergen.
Conclusions
It is concluded that this IgE-hyporeactive molecule can be produced in folded form and that it is able to induce an antibody response that efficiently competes with IgE recognition of Phl p 1. These findings suggest that it, or a further evolved variant thereof, is a candidate for use as a component in specific immunotherapy against grass pollen allergy.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0150-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0150-z
PMCID: PMC4460866  PMID: 26054338
Group 1 grass pollen allergen; Hypoallergen; IgE; Immunogenicity; Production; Protein fold
19.  Continuous enhancement of iturin A production by Bacillus subtilis with a stepwise two-stage glucose feeding strategy 
BMC Biotechnology  2015;15:53.
Background
The lipopeptide antibiotic iturin A is an attractive biopesticide with the potential to replace chemical-based pesticides for controlling plant pathogens. However, its industrial fermentation has not been realized due to the high production costs and low product concentrations. This study aims to enhance iturin A production by performing a novel fermentation process with effective glucose feeding control using rapeseed meal as a low-cost nitrogen source.
Results
We demonstrated that continuous and significant enhancement of iturin A production could be achieved by a novel two-stage glucose-feeding strategy with a stepwise decrease in feeding rate. Using this strategy, the ratio of spores to total cells could be maintained at a desirable/stable level of 0.80–0.86, and the reducing sugar concentration could be controlled at a low level of 2–3 g/L so that optimal substrate balance could be maintained throughout the feeding phase. As a result, the maximum iturin A concentration reached 1.12 g/L, which was two-fold higher than that of batch culture.
Conclusions
This is the first report which uses control of the glucose supply to improve iturin A production by fed-batch fermentation and identifies some important factors necessary to realize industrial iturin A production. This approach may also enhance the production of other useful secondary metabolites by Bacillus subtilis.
doi:10.1186/s12896-015-0172-6
PMCID: PMC4460961  PMID: 26054393
Bacillus subtilis; Iturin A; Lipopeptide; Rapeseed meal; Fed-batch fermentation
20.  Improved detection of Escherichia coli and coliform bacteria by multiplex PCR 
BMC Biotechnology  2015;15:48.
Background
The presence of coliform bacteria is routinely assessed to establish the microbiological safety of water supplies and raw or processed foods. Coliforms are a group of lactose-fermenting Enterobacteriaceae, which most likely acquired the lacZ gene by horizontal transfer and therefore constitute a polyphyletic group. Among this group of bacteria is Escherichia coli, the pathogen that is most frequently associated with foodborne disease outbreaks and is often identified by β-glucuronidase enzymatic activity or by the redundant detection of uidA by PCR. Because a significant fraction of essential E. coli genes are preserved throughout the bacterial kingdom, alternative oligonucleotide primers for specific E. coli detection are not easily identified.
Results
In this manuscript, two strategies were used to design oligonucleotide primers with differing levels of specificity for the simultaneous detection of total coliforms and E. coli by multiplex PCR. A consensus sequence of lacZ and the orphan gene yaiO were chosen as targets for amplification, yielding 234 bp and 115 bp PCR products, respectively.
Conclusions
The assay designed in this work demonstrated superior detection ability when tested with lab collection and dairy isolated lactose-fermenting strains. While lacZ amplicons were found in a wide range of coliforms, yaiO amplification was highly specific for E. coli. Additionally, yaiO detection is non-redundant with enzymatic methods.
doi:10.1186/s12896-015-0168-2
PMCID: PMC4453288  PMID: 26040540
Multiplex PCR; Coliform detection; Escherichia coli identification
21.  A simple and efficient seamless DNA cloning method using SLiCE from Escherichia coli laboratory strains and its application to SLiP site-directed mutagenesis 
BMC Biotechnology  2015;15:47.
Background
Seamless ligation cloning extract (SLiCE) is a simple and efficient method for DNA assembly that uses cell extracts from the Escherichia coli PPY strain, which expresses the components of the λ prophage Red/ET recombination system. This method facilitates restriction endonuclease cleavage site-free DNA cloning by performing recombination between short stretches of homologous DNA (≥15 base pairs).
Results
To extend the versatility of this system, I examined whether, in addition to bacterial extracts from the PPY strain, other E. coli laboratory strains were suitable for the SLiCE protocol. Indeed, carefully prepared cell extracts from several strains exhibited sufficient cloning activity for seamless gene incorporation into vectors with short homology lengths (approximately 15–20 bp). Furthermore, SLiCE was applied to the polymerase chain reaction (PCR)-based site-directed mutagenesis method, in a process termed “SLiCE-mediated PCR-based site-directed mutagenesis (SLiP site-directed mutagenesis)”. SLiP site-directed mutagenesis simplifies the steps of PCR-based site-directed mutagenesis, as it exploits the capability of the SLiCE method to insert multiple fragments.
Conclusions
SLiCE can be performed in the laboratory with no requirement for a special E. coli strain, and the technique is easily established. This method increases the cloning efficiency, shortens the time for DNA manipulation, and greatly reduces the cost of seamless DNA cloning.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0162-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0162-8
PMCID: PMC4453199  PMID: 26037246
Homologous recombination; Seamless DNA cloning; SLiCE; Site-directed mutagenesis; Plant redox-related gene
22.  Engineering selection stringency on expression vector for the production of recombinant human alpha1-antitrypsin using Chinese Hamster ovary cells 
BMC Biotechnology  2015;15:44.
Background
Expression vector engineering technology is one of the most convenient and timely method for cell line development to meet the rising demand of novel production cell line with high productivity. Destabilization of dihydrofolate reductase (dhfr) selection marker by addition of AU-rich elements and murine ornithine decarboxylase PEST region was previously shown to improve the specific productivities of recombinant human interferon gamma in CHO-DG44 cells. In this study, we evaluated novel combinations of engineered motifs for further selection marker attenuation to improve recombinant human alpha-1-antitrypsin (rhA1AT) production. Motifs tested include tandem PEST elements to promote protein degradation, internal ribosome entry site (IRES) mutations to impede translation initiation, and codon-deoptimized dhfr selection marker to reduce translation efficiency.
Results
After a 2-step methotrexate (MTX) amplification to 50 nM that took less than 3 months, the expression vector with IRES point mutation and dhfr-PEST gave a maximum titer of 1.05 g/l with the top producer cell pool. Further MTX amplification to 300 nM MTX gave a maximum titer of 1.15 g/l. Relative transcript copy numbers and dhfr protein expression in the cell pools were also analysed to demonstrate that the transcription of rhA1AT and dhfr genes were correlated due to the IRES linkage, and that the strategies of further attenuating dhfr protein expression with the use of a mutated IRES and tandem PEST, but not codon deoptimization, were effective in reducing dhfr protein levels in suspension serum free culture.
Conclusions
Novel combinations of engineered motifs for further selection marker attenuation were studied to result in the highest reported recombinant protein titer to our knowledge in shake flask batch culture of stable mammalian cell pools at 1.15 g/l, highlighting applicability of expression vector optimization in generating high producing stable cells essential for recombinant protein therapeutics production. Our results also suggest that codon usage of the selection marker should be considered for applications that may involve gene amplification and serum free suspension culture, since the overall codon usage and thus the general expression and regulation of host cell proteins may be affected in the surviving cells.
Electronic supplementary material
The online version of this article (doi:10.1186/s12896-015-0145-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12896-015-0145-9
PMCID: PMC4450478  PMID: 26033090
Expression vector; Selection stringency; Dihydrofolate reductase; Alpha1-antitrypsin; Internal ribosome entry site; Codon deoptimization
23.  Active immunization with Tocilizumab mimotopes induces specific immune responses 
BMC Biotechnology  2015;15:46.
Background
Tocilizumab is a humanized monoclonal antibody showing high-affinity binding to both soluble interleukin-6 receptor (sIL-6R) and membrane bound IL-6R (mIL-6R), thereby preventing pro-inflammatory effects of IL-6. However, therapeutic antibodies still have practical limitations. To overcome these limitations, we generated Tocilizumab specific epitope mimics by using the phage display technology and tested whether the peptide mimics could induce similar humoral responses in mice immunized with the peptides.
Results
Seven phage mimics were obtained by using phage display peptide library. Four phage mimics (YHTTDKLFYMMR, YSAYEFEYILSS, KTMSAEEFDNWL and LTSHTYRSQADT) were shown to mimic Tocilizumab epitope using immunoassays. The mimotopes were conjugated to immunogenic carrier proteins and used to intraperitoneally immunize BALB/c mice. Sera from the mimotopes immunized mice not only showed specific binding to recombinant IL-6R, but can also IL-6R expressed in Hela, U-937, Jurkat cell lines and in fibroblast-like synoviocytes from patients with RA (FLS-RA). Furthermore, sera from mice immunized with mimotopes-KLH conjugate could reduce the level of phosphorylated- signal transducers and activator of transcription (STAT3), STAT3, phosphorylated- extracellular signal-regulated kinase (Erk) 1/2 and Erk1/2 in HeLa and Jurkat cells. Antibody-dependent cellular cytotoxicity (ADCC) assay showed that antibodies induced by mimotopes-KLH conjugate could elicit specific lysis in Hela and U-937 cells.
Conclusions
From phage display library, we successfully isolated four Tocilizumab mimotopes which induced specific humoral and cellular reponses in vitro and in vivo.
doi:10.1186/s12896-015-0161-9
PMCID: PMC4450830  PMID: 26033236
Rheumatoid arthritis; Tocilizumab; Mimotope; IL-6; Phage display
24.  Production of oleanane-type sapogenin in transgenic rice via expression of β-amyrin synthase gene from Panax japonicus C. A. Mey 
BMC Biotechnology  2015;15:45.
Background
Panax japonicus C. A. Mey. is a rare traditional Chinese herbal medicine that uses ginsenosides as its main active ingredient. Rice does not produce ginsenosides because it lacks a key rate-limiting enzyme (β-amyrin synthase, βAS); however, it produces a secondary metabolite, 2,3-oxidosqualene, which is a precursor for ginsenoside biosynthesis.
Results
In the present study, the P. japonicus βAS gene was transformed into the rice cultivar ‘Taijing 9’ using an Agrobacterium-mediated approach, resulting in 68 rice transgenic plants of the T0 generation. Transfer-DNA (T-DNA) insertion sites in homozygous lines of the T2 generation were determined by using high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR) and were found to vary among the tested lines. Approximately 1–2 copies of the βAS gene were detected in transgenic rice plants. Real-time PCR and Western blotting analyses showed that the transformed βAS gene could be overexpressed and β-amyrin synthase could be expressed in rice. HPLC analysis showed that the concentration of oleanane-type sapogenin oleanolic acid in transgenic rice was 8.3–11.5 mg/100 g dw.
Conclusions
The current study is the first report on the transformation of P. japonicus βAS gene into rice. We have successfully produced a new rice germplasm, “ginseng rice”, which produces oleanane-type sapogenin.
doi:10.1186/s12896-015-0166-4
PMCID: PMC4450844  PMID: 26033328
Ginsenosides; Sapogenin; β-amyrin synthase gene; Rice; Genetic transformation
25.  Application of M13 phage display for identifying immunogenic proteins from tick (Ixodes scapularis) saliva 
BMC Biotechnology  2015;15:43.
Background
Ticks act as vectors for a large number of different pathogens, perhaps most notably Borrelia burgdorferi, the causative agent of Lyme disease. The most prominent tick vector in the United States is the blacklegged tick, Ixodes scapularis. Tick bites are of special public health concern since there are no vaccines available against most tick-transmitted pathogens. Based on the observation that certain non-natural host animals such as guinea pigs or humans can develop adaptive immune responses to tick bites, anti-tick vaccination is a potential approach to tackle health risks associated with tick bites.
Results
The aim of this study was to use an oligopeptide phage display strategy to identify immunogenic salivary gland proteins from I. scapularis that are recognized by human immune sera. Oligopeptide libraries were generated from salivary gland mRNA of 18 h fed nymphal I. scapularis. Eight immunogenic oligopeptides were selected using human immune sera. Three selected immunogenic oligopeptides were cloned and produced as recombinant proteins. The immunogenic character of an identified metalloprotease (MP1) was validated with human sera. This enzyme has been described previously and was hypothesized as immunogenic which was confirmed in this study. Interestingly, it also has close homologs in other Ixodes species.
Conclusion
An immunogenic protein of I. scapularis was identified by oligopeptide phage display. MP1 is a potential candidate for vaccine development.
doi:10.1186/s12896-015-0167-3
PMCID: PMC4449557  PMID: 26024663

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