Design and development of low cost polyurethane biopolymer based on castor oil and glycerol for biomedical applications

In the current study, we present the synthesis of novel low cost bio‐polyurethane compositions with variable mechanical properties based on castor oil and glycerol for biomedical applications. A detailed investigation of the physicochemical properties of the polymer was carried out by using mechanical testing, ATR‐FTIR, and X‐ray photoelectron spectroscopy (XPS). Polymers were also tested in short term in‐vitro cell culture with human mesenchymal stem cells to evaluate their biocompatibility for potential applications as biomaterial. FTIR analysis confirmed the synthesis of castor oil and glycerol based PU polymers. FTIR also showed that the addition of glycerol as co‐polyol increases crosslinking within the polymer backbone hence enhancing the bulk mechanical properties of the polymer. XPS data showed that glycerol incorporation leads to an enrichment of oxidized organic species on the surface of the polymers. Preliminary investigation into in vitro biocompatibility showed that serum protein adsorption can be controlled by varying the glycerol content with polymer backbone. An alamar blue assay looking at the metabolic activity of the cells indicated that castor oil based PU and its variants containing glycerol are non‐toxic to the cells. This study opens an avenue for using low cost bio‐polyurethane based on castor oil and glycerol for biomedical applications.     

Tools for the discovery of biopolymer producing cysteine relays

Cysteine relays, where a protein or small molecule is transferred multiple times via transthiolation, are central to the production of biological polymers. Enzymes that utilise relay mechanisms display broad substrate specificity and are readily engineered to produce new polymers. In this review, I discuss recent advances in the discovery, engineering and biophysical characterisation of cysteine relays. I will focus on eukaryotic ubiquitin (Ub) cascades and prokaryotic polyhydroxyalkanoate (PHA) synthesis. These evolutionarily distinct processes employ similar chemistry and are readily modified for biotechnological applications. Both processes have been studied intensively for decades, yet recent studies suggest we do not fully understand their mechanistic diversity or plasticity. I will discuss the important role that activity-based probes (ABPs) and other chemical tools have had in identifying and delineating Ub cysteine-relays and the potential for ABPs to be applied to PHA synthases. Finally, I will offer a personal perspective on the potential of engineering cysteine-relays for non-native polymer production.     

Effective recovery of poly‐β‐hydroxybutyrate (PHB) biopolymer from Cupriavidus necator using a novel and environmentally friendly solvent system

This work demonstrates a significant advance in bioprocessing for a high‐melting lipid polymer. A novel and environmental friendly solvent mixture, acetone/ethanol/propylene carbonate (A/E/P, 1:1:1 v/v/v) was identified for extracting poly‐hydroxybutyrate (PHB), a high‐value biopolymer, from Cupriavidus necator. A set of solubility curves of PHB in various solvents was established. PHB recovery of 85% and purity of 92% were obtained from defatted dry biomass (DDB) using A/E/P. This solvent mixture is compatible with water, and from non‐defatted wet biomass, PHB recovery of 83% and purity of 90% were achieved. Water and hexane were evaluated as anti‐solvents to assist PHB precipitation, and hexane improved recovery of PHB from biomass to 92% and the purity to 93%. A scale‐up extraction and separation reactor was designed, built and successfully tested. Properties of PHB recovered were not significantly affected by the extraction solvent and conditions, as shown by average molecular weight (1.4 × 10⁶) and melting point (175.2°C) not being different from PHB extracted using chloroform. Therefore, this biorenewable solvent system was effective and versatile for extracting PHB biopolymers. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:678–685, 2016     

Characterizing a stable methane-utilizing mixed culture used in the synthesis of a high-quality biopolymer in an open system

AIMS: To characterize a methane-utilizing poly-beta-hydroxybutyrate (PHB)-producing microbial community. METHODS AND RESULTS: Three different approaches based on microbiology, analytical chemistry and molecular biology were used to determine the composition of the mixed culture. The dominant species, Methylocystis sp. GB25, represents more than 86% of the total biomass. Seven accompanying bacterial species are present in the mixed culture of which two are methylotrophic bacteria and five are utilizers of complex carbon sources. Both these groups were found to be present at the same ratio with respect to each other. Results of fatty acid analysis and PCR-DGGE fingerprints reflect the stability of the mixed-culture composition in the open system during multiple continuous growth and polymer formation processes throughout a period of 29 months. The consistently high quality of the accumulated polymer further corroborates this finding. CONCLUSION: The methane-utilizing mixed culture has the potential of self-regulation resulting in a stable composition even under non-aseptic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: Avoiding the necessity of sterile conditions, as demonstrated in this paper, is an important step towards the development of a viable large-scale process for the production of PHB using cheap substrates like methane from natural or renewable sources. This is the first report characterizing a bacterial mixed culture being used for the biotechnological production of a high-value product in an open system.     

<Emphasis Type="Italic">Alkaliphilus peptidofermentans</Emphasis> sp. nov., a new alkaliphilic bacterial soda lake isolate capable of peptide fermentation and Fe(III) reduction

A novel strain, Z-7036, of anaerobic spore-forming bacteria was isolated from a cellulolytic consortium obtained from the bottom sediments of the low-mineralization soda lake Verkhnee Beloe (Buryatia). The cells of the new strain are short motile gram-positive rods, 1.1–3.0 × 0.25–0.4 μm. The organism is an aerotolerant anaerobe and obligate alkaliphile growing within the pH range of 7.5–9.7 with an optimum at pH 9.1. The strain is mesophilic and halotolerant and grows at NaCl concentrations from 0 to 50 g/l with an optimum at 20 g/l. Carbonates are required. The microorganism ferments peptone, yeast extract, trypticase, tryptone, Bacto Soytone, meat extract, Casamino acids, ornithine, arginine, threonine, and tryptophan. The strain hydrolyzes the bacterial preparations “Gaprin” and “Spirulina”. Acetate and formate are the major fermentation products. The strain reduces amorphous ferric hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), S₂O ₃ ^2? , fumarate, and crotonate. Major fatty acids are C_16:0, C1_6:1ω7c, iso-C₁₇, iso-C₁₅, and iso-C_17:1. The DNA G+C content is 33.8 ± 0.5 mol %. According to the results of the 16S rRNA gene analysis, strain Z-7036 belongs to the genus Alkaliphilus within the cluster XI of low G+C gram-positive bacteria of the family Clostridiaceae. The novel strain is closely related to A. transvaalensis SAGM1^T and A. crotonatoxidans B11-2^T (93.3 and 93.9% 16S rRNA sequence identities, respectively). On the basis of the existing genotypic and phenotypic differences, we propose that strain Z-7036 should be classified as a novel species Alkaliphilus peptidofermentans sp. nov.     

Development of a novel spatiotemporal depletion system for cellular cholesterol

Cholesterol is an essential component of mammalian cell membranes whose subcellular concentration and function are tightly regulated by de novo biosynthesis, transport, and storage. Although recent reports have suggested diverse functions of cellular cholesterol in different subcellular membranes, systematic investigation of its site-specific roles has been hampered by the lack of a methodology for spatiotemporal manipulation of cellular cholesterol levels. Here, we report the development of a new cholesterol depletion system that allows for spatiotemporal manipulation of intracellular cholesterol levels. This system utilizes a genetically encoded cholesterol oxidase whose intrinsic membrane binding activity is engineered in such a way that its membrane targeting can be controlled in a spatiotemporally specific manner via chemically induced dimerization. In combination with in situ quantitative imaging of cholesterol and signaling activity measurements, this system allows for unambiguous determination of site-specific functions of cholesterol in different membranes, including the plasma membrane and the lysosomal membrane.     

Development of a novel bacterial artificial chromosome cloning system for functional studies

Bacterial artificial chromosome (BAC) cloning systems currently in use generate high quality genomic libraries for gene mapping, identification, and sequencing. However, the most commonly used BAC cloning systems do not facilitate functional studies in eukaryotic cells. To overcome this limitation, we have developed pEBAC190G, a new BAC vector that combines the features of the first generation PAC/BAC vectors with eukaryotic elements that facilitate the transfection, episomal maintenance, and functional analysis of large genomic fragments in eukaryotic cells. A number of different cloning strategies may be used to retrofit genomic fragments from existing libraries into the new vector. The system was tested by the retrofitting of a 170kb NotI genomic fragment from the RPCI-11 BAC library into the NotI site of pEBAC190G. Clones from any eukaryotic genomic library harboured in this vector can be transferred from bacteria directly to eukaryotic cells for functional analysis.     

Development of a standard bacterial consortium for laboratory efficacy testing of commercial freshwater oil spill bioremediation agents

Six crude oil-degrading bacterial strains isolated from different soil and water environments were combined to create a defined consortium for use in standardized efficacy testing of commercial oil spill bioremediation agents (OSBA). The isolates were cryopreserved in individual aliquots at pre-determined cell densities, stored at −70°C, and thawed for use as standardized inocula as needed. Aliquots were prepared with precision (typically within 10% of the mean) ensuring reproducible inoculation. Five of the six strains displayed no appreciable loss of viability during cryopreservation exceeding 2.5 years, and five isolates demonstrated stable hydrocarbon-degrading phenotypes during inoculum preparation and storage. When resuscitated, the defined consortium reproducibly biodegraded Alberta Sweet Mixed Blend crude oil (typically ± 7% of the mean of triplicate cultures), as determined by quantitative gas chromatography–mass spectrometry of various analyte classes. Reproducible biodegradation was observed within a batch of inoculum in trials spanning 2.5 years, and among three batches of inoculum prepared more than 2 years apart. Biodegradation was comparable after incubation for 28 days at 10°C or 14 days at 22°C, illustrating the temperature tolerance of the bacterial consortium. The results support the use of the synthetic consortium as a reproducible, predictable inoculum to achieve standardized efficacy tests for evaluating commercial OSBA. Received 31 August 1998/ Accepted in revised form 30 November 1998     

Evaluation of rheological properties of the exopolysaccharide of Sphingomonas paucimobilis GS-1 for application in oil exploration

Analysis of an exopolysaccharide of Sphingomonas paucimobilis GS-1 (EPS/GS-1) with respect to its rheological properties, cross-linking ability with chrome alum and performance test at 75 ± 5°C revealed its strong suspending ability, shear thinning property, and thixotrophic nature which are required to impart desirable rheology to drilling mud. The organism fulfilled all the specified requirements and its properties were superior to those of currently-used XC polymer (a xanthan product) for oil drilling applications. However, EPS/GS-1 was unstable in the presence of bentonite at 100 ± 5°C during performance tests, in contrast to XC polymer. Received 14 April 1999/ Accepted in revised form 26 July 1999     

Development of a method for the application of solid-phase microextraction to monitor biodegradation of volatile hydrocarbons during bacterial growth on crude oil

A quantitative solid-phase microextraction, gas chromatography, flame ionization detector (SPME-GC-FID) method for low-molecular-weight hydrocarbons from crude oil was developed and applied to live biodegradation samples. Repeated sampling was achieved through headspace extractions at 30°C for 45 min from flasks sealed with Teflon Mininert. Quantification without detailed knowledge of oil–water–air partition coefficients required the preparation of standard curves. An inverse relationship between retention time and mass accumulated on the SPME fibre was noted. Hydrocarbons from C₅ to C₁₆ were dated and those up to C₁₁ were quantified. Total volatiles were quantified using six calibration curves. Biodegradation of volatile hydrocarbons during growth on crude oil was faster and more complete with a mixed culture than pure isolates derived therefrom. The mixed culture degraded 55% of the compounds by weight in 4 days versus 30–35% by pure cultures of Pseudomonas aeruginosa, Rhodococcus globerulus or a co-culture of the two. The initial degradation rate was threefold higher for the mixed culture, reaching 45% degradation after 48 h. For the mixed culture, the degradation rate of individual alkanes was proportional to the initial concentration, decreasing from hexane to undecane. P. fluorescens was unable to degrade any of the low-molecular-weight hydrocarbons and methylcyclohexane was recalcitrant in all cases. Overall, the method was found to be reliable and cost-effective. Journal of Industrial Microbiology & Biotechnology (2000) 25, 155–162. Received 04 March 2000/ Accepted in revised form 25 June 2000     

Isolation,screening, and optimization of bacterial strains for novel transglutaminase production

Transglutaminases are a class of transferases known to form isopeptide bond between glutamine and lysine residues in a protein molecule. Increasing demand for transglutaminase in food and other industries and its low productivity have compelled researchers to isolate and screen micro-organisms with potential to produce it. In the present investigation around 200 isolates were screened for extracellular secretion of microbial transglutaminase (MTGase). Isolate B4 showed enzyme activity of 1.71?±?0.2?U/mL followed by isolate C2 which showed 1.61?±?0.17?U/mL activity, comparable with the activity of industrially used microbial strains. Biochemical analysis along with 16S r-RNA sequencing revealed these isolates (B4 and C2) to be Bacillus nakamurai and a variant of Bacillus subtilis, respectively. Amongst the various production media screened, a medium containing starch and peptone was found best for MTGase production. Correlation between growth, enzyme production, and sugar utilization was also studied and maximum enzyme production was obtained after 48 to 60?hr. Highest MTGase titer (3.95?±?0.03?U/mL for B4 and 2.65?±?0.17?U/mL for C2) was obtained by optimization of parameters. The enzyme was characterized for temperature and pH optima, pH and thermal stability, and effect of metal ions, suggesting its potential use in future applications.     

Design of a novel system for the construction of vectors for Agrobacterium-mediated plant transformation

Summary The loxP-Cre site-specific recombination system of phage P1 was used to develop a novel strategy to construct cointegrate vectors for Agrobacterium-mediated plant transformation. A pTi disarmed helper plasmid (pAL1166) was constructed by replacing the oncogenic T-DNA by a loxP sequence and a spectinomycin resistance marker in the octopine-type pTiB6 plasmid. The cre gene was cloned into an unstable incP plasmid. A third plasmid, which did not replicate in Agrobacterium and contained another loxP sequence together with a kanamycin resistance marker, was used to test the system. Electroporation of this third plasmid into an Agrobacterium strain harbouring both pAL1166 and the Cre-encoding plasmid resulted in kanamycin-resistant cells containing a cointegrate between pAL1166 and the incoming plasmid. Cointegration occurred by Cre-mediated recombination at the loxP sites, and the cointegrate was stabilized in the Agrobacterium cells by the loss of the Cre-encoding plasmid shortly after the recombination event had taken place.     

Highly fluorescent carbon dots from wheat bran as a novel drug delivery system for bacterial inhibition

In this study, we prepared carbon dots (CDs) from wheat bran via hydrothermal treatment at 180°C for 3 h. The prepared CDs showed blue‐green fluorescence under UV light. The fluorescence emission study of the CDs revealed that they showed maximum fluorescence emission at 500 nm. The prepared CDs showed a high quantum yield of 33.23%. Solvent‐dependent fluorescence emission analysis of the CDs was performed to study the variation in fluorescence emission characteristics with solvent polarity. The prepared CDs were conjugated with amoxicillin (AMX) to explore its potential for use as a drug delivery agent for AMX. The drug release profile of the CD–AMX conjugates was analyzed at different pH (5.0, 6.8 and 7.2) to study drug release kinetics. CD–AMX conjugates showed notable bacterial inhibition against Gram‐positive (S. aureus) and Gram‐negative (E. coli) strains with minimal cytotoxic effects, indicating its potential as a promising antibacterial drug delivery system.     

Evidence for a novel domain of bacterial outer membrane ushers

Many pathogenic bacteria possess adhesive surface organelles (called pili), anchored to their outer membrane, which mediate the first step of infection by binding to host tissue. Pilus biogenesis occurs via the "chaperone-usher" pathway: the usher, a large outer membrane protein, binds complexes of a periplasmic chaperone with pilus subunits, unloads the subunits from the chaperone, and assembles them into the pilus, which is extruded into the extracellular space. Ushers comprise an N-terminal periplasmic domain, a large transmembrane beta-barrel central domain, and a C-terminal periplasmic domain. Since structural data are available only for the N-terminal domain, we performed an in-depth bioinformatic analysis of bacterial ushers. Our analysis led us to the conclusion that the transmembrane beta-barrel region of ushers contains a so far unrecognized soluble domain, the "middle domain", which possesses a beta-sandwich fold. Two other bacterial beta-sandwich domains, the TT0351 protein from Thermus thermophilus and the carbohydrate binding module CBM36 from Paenibacillus polymyxa, are possible distant relatives of the usher "middle domain". Several mutations reported to abolish in vivo pilus formation cluster in this region, underlining its functional importance.     

Design of a novel automated methanol feed system for pilot-scale fermentation of Pichia pastoris

Large-scale fermentation of Pichia pastoris requires a large volume of methanol feed during the induction phase. However, a large volume of methanol feed is difficult to use in the processing suite because of the inconvenience of constant monitoring, manual manipulation steps, and fire and explosion hazards. To optimize and improve safety of the methanol feed process, a novel automated methanol feed system has been designed and implemented for industrial fermentation of P. pastoris. Details of the design of the methanol feed system are described. The main goals of the design were to automate the methanol feed process and to minimize the hazardous risks associated with storing and handling large quantities of methanol in the processing area. The methanol feed system is composed of two main components: a bulk feed (BF) system and up to three portable process feed (PF) systems. The BF system automatically delivers methanol from a central location to the portable PF system. The PF system provides precise flow control of linear, step, or exponential feed of methanol to the fermenter. Pilot-scale fermentations with linear and exponential methanol feeds were conducted using two Mut(+) (methanol utilization plus) strains, one expressing a recombinant therapeutic protein and the other a monoclonal antibody. Results show that the methanol feed system is accurate, safe, and efficient. The feed rates for both linear and exponential feed methods were within ± 5% of the set points, and the total amount of methanol fed was within 1% of the targeted volume.     

A novel manual pooling system for preparing three-dimensional pools of a deep coverage soybean bacterial artificial chromosome library

Compared with hybridization‐based techniques, polymerase chain reaction‐based screening of large insert libraries has been used widely as it is fast, easy and sensitive. However, various pooling strategies are needed to ensure efficient screening. It is time‐consuming and labourious to prepare three‐dimensional pools for a deep coverage bacterial artificial chromosome (BAC) library of soybean (1.12 × 10⁹ bp) in the absence of robotic facility. In the present study, we describe a novel manual pooling system for preparing three‐dimensional pools of a soybean BAC library. This simple technique enables a single researcher to construct three‐dimensional pools for a deep‐coverage (12 haploid genome equivalents) BAC library of soybean in less than 2 months without any robotic manipulation. When the prepared three‐dimensional pools were screened with 29 polymerase chain reaction‐based markers, an average of 9.2 clones per marker were identified. These identified clones will be useful either in quantitative trait loci gene isolation or in synteny study between soybean and other legumes including Lotus japonicus. This efficient pooling system could be applied to any other BAC libraries without the need for robotic manipulation.     

Design,synthesis and identification of N,N-dibenzylcinnamamide (DBC) derivatives as novel ligands for α-synuclein fibrils by SPR evaluation system

PET imaging of α-synuclein (α-syn) deposition in the brain will be an effective tool for earlier diagnosis of Parkinson's disease (PD) due to α-syn aggregation is the widely accepted biomarker for PD. However, the necessary PET radiotracer for imaging is clinically unavailable until now. The lead compound discovery is the first key step for the study. Herein, we initially established an efficient biologically evaluation system well in high throughput based on SPR technology, and identified a novel class of N, N-dibenzylcinnamamide (DBC) compounds as α-syn ligands through the assay. These compounds were proved to have high affinities against α-syn aggregates (K_D < 10 nM), which well met the requirement of binding activity for the PET probe. These DBC compounds were firstly reported as α-syn ligands herein and the preliminary obtained structure has been further modified into F-labeled ones. Among them, a high-affinity tracer (5–41) with 1.03 nM (K_D) has been acquired, indicating its potential as a new lead compound for developing PET radiotracer.     

Characterization of a novel unique restriction-modification system from Yersinia enterocolitica O:8 1B

Genetic manipulations with enteropathogenic Yersinia enterocolitica O:8 are complicated by the presence of an efficient PstI-like YenI restriction-modification (R-M) system. We have characterized the YenI R-M system in Y. enterocolitica O:8, biotype 1B. A 5039 bp DNA fragment of the pSAK2 recombinant plasmid carrying the yenI locus was used to determine the nucleotide sequence. DNA sequence analysis identified a single 2481 bp open reading frame (ORF) that encodes an 826 amino acid large polypeptide having an apparent molecular mass of 93 kDa. The N-terminal part of the YenI ORF has 45 and 40% identity to PstI and BsuI methyltransferases (MTases), respectively; while the C-terminal part depicts 55 and 45% identity to endonucleases (ENases) of both isoschyzomeric enzymes. The yenI gene was cloned into pT7-5 plasmid and has been shown to encode a single polypeptide of expected molecular mass. A specific recognition sequence, typical to the type II R-M systems and single peptide organization, typical to type IV R-M systems, make YenI unique among known restriction-modification systems. We have constructed a truncated recombinant variant of YenI enzyme, which conserved only MTase activity, and that can be applied to YenI methylation of the DNA to be transformed into Y. enterocolitica O:8 biotype 1B strains.     

Effect of nitrate injection on the bacterial community in a water-oil tank system analyzed by PCR-DGGE

Sulfide production by sulfate-reducing bacteria (SRB) is a major concern for the petroleum industry since it is toxic and corrosive, and causes plugging due to the formation of insoluble iron sulfides (reservoir souring). In this study, PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) using two sets of primers based on the 16S rRNA gene and on the aps gene (adenosine-5-phosphosulfate reductase) was used to track changes in the total bacterial and SRB communities, respectively, present in the water-oil tank system on an offshore platform in Brazil in which nitrate treatment was applied for 2 months (15 nitrate injections). PCR-DGGE analysis of the total bacterial community showed the existence of a dominant population in the water-oil tank, and that the appearance and/or the increase of intensity of some bands in the gels were not permanently affected by the introduction of nitrate. On the other hand, the SRB community was stimulated following nitrate treatment. Moreover, sulfide production did not exceed the permissible exposure limit in the water-oil separation tank studied treated with nitrate. Therefore, controlling sulfide production by treating the produced water tank with nitrate could reduce the quantity of chemical biocides required to control microbial activities.