In silico screening and heterologous expression of soluble dimethyl sulfide monooxygenases of microbial origin in Escherichia coli.

Sequence-based screening has been widely applied in the discovery of novel microbial enzymes. However, majority of the sequences in the genomic databases were annotated using computational approaches and lacks experimental characterization. Hence, the success in obtaining the functional biocatalysts with improved characteristics requires an efficient screening method that considers a wide array of factors. Recombinant expression of microbial enzymes is often hampered by the undesirable formation of inclusion body. Here, we present a systematic in silico screening method to identify the proteins expressible in soluble form and with the desired biological properties. The screening approach was adopted in the recombinant expression of dimethyl sulfide (DMS) monooxygenase in Escherichia coli. DMS monooxygenase, a two-component enzyme consisting of DmoA and DmoB subunits, was used as a model protein. The success rate of producing soluble and active DmoA is 71% (5 out of 7 genes). Interestingly, the soluble recombinant DmoA enzymes exhibited the NADH:FMN oxidoreductase activity in the absence of DmoB (second subunit), and the cofactor FMN, suggesting that DmoA is also an oxidoreductase. DmoA originated from Janthinobacterium sp. AD80 showed the maximum NADH oxidation activity (maximum reaction rate: 6.6 µM/min; specific activity: 133 µM/min/mg). This novel finding may allow DmoA to be used as an oxidoreductase biocatalyst for various industrial applications. The in silico gene screening methodology established from this study can increase the success rate of producing soluble and functional enzymes while avoiding the laborious trial and error involved in the screening of a large pool of genes available. KEY POINTS: • A systematic gene screening method was demonstrated. • DmoA is also an oxidoreductase capable of oxidizing NADH and reducing FMN. • DmoA oxidizes NADH in the absence of external FMN.

Proton-Functionalized Graphitic Carbon Nitride for Efficient Metal-Free Destruction of Escherichia coli under Low-Power Light Irradiation.

Universal access to clean water has been a global ambition over the years. Photocatalytic water disinfection through advanced oxidation processes has been regarded as one of the promising methods for breaking down microbials. The forefront of this research focuses on the application of metal-free photocatalysts for disinfection to prevent secondary pollution. Graphitic carbon nitride (g-C3 N4 ) has achieved instant attention as a metal-free and visible-light-responsive photocatalyst for various energy and environmental applications. However, the photocatalytic efficiency of g-C3 N4 is still affected by its rapid charge recombination and sluggish electron-transfer kinetics. In this contribution, two-dimensionally protonated g-C3 N4 was employed as metal-free photocatalyst for water treatment and demonstrated 100 % of Escherichia coli within 4 h under irradiation with a 23 W light bulb. The introduction of protonation can modulate the surface charge of g-C3 N4 ; this enhances its conductivity and provides a "highway" for the delocalization of electrons. This work highlights the potential of conjugated polymers in antibacterial application.

Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches.

Over the past few decades, Escherichia coli (E. coli) remains the most favorable host among the microbial cell factories for the production of soluble recombinant proteins. Recombinant protein production (RPP) via E. coli is optimized at the level of gene expression (expression level) and the process condition of fermentation (process level). Presently, the reported studies do not give a clear view on the selection of methods employed in the optimization of RPP. Here, we have reviewed various optimization methods and their preferences with respect to the factors at expression and process levels to achieve the optimal levels of soluble RPP. With a greater understanding of these optimization methods, we proposed a stepwise methodology linking the factors from both levels for optimizing the production of soluble recombinant protein in E. coli. The proposed methodology is further explained through five sets of examples demonstrating the optimization of RPP at both expression and process levels.Key Points• Stepwise methodology of optimizing recombinant protein production is proposed.• In silico tools can facilitate the optimization of gene- and protein-based factors.• Optimization of gene- and protein-based factors aids host-vector selection.• Statistical optimization is preferred for achieving optimal levels of process factors.

Recent development and challenges in extraction of phytonutrients from palm oil.

Phytonutrients are plant-derived bioactives which are widely utilized as colorants or supplements in food, cosmetic, and pharmaceutical products. To meet the global demand for phytonutrients, oil palm has emerged as a promising source of phytonutrients on account of its large-scale plantation worldwide and high oil productivity. Phytonutrients including carotenoids, tocols, sterols, squalene, phospholipids, coenzyme Q10, and polyphenols can be found in crude palm oil as well as in the byproducts (e.g. palm oil mill effluent and palm-pressed fiber oil) generated from the palm oil milling process. However, the high viscosity and semisolid properties of palm oil are problematic in phytonutrient extraction. Another major challenge is the retention of the sensitive phytonutrients during the extraction process. Over the years, the advances in the extraction methods have improved the extractability of phytonutrients. The emerging extraction methods can operate under mild conditions to mitigate the risk of phytonutrient degradation. This review outlines the types of phytonutrient in palm oil and their extraction strategies. The working principles and operating conditions of extraction methods are discussed along with their potential and limitations in terms of extraction efficiency and practicability. The methods for pretreatment of feedstocks for improving extraction efficiency are also highlighted. The challenges in the extraction of phytonutrient from palm oil feedstock are summarized. Lastly, we provide suggestions for overcoming the limitations and improving the performances of phytonutrient extraction.

Size-selective purification of hepatitis B virus-like particle in flow-through chromatography: Types of ion exchange adsorbent and grafted polymer architecture.

Hepatitis B virus-like particles expressed in Escherichia coli were purified using anion exchange adsorbents grafted with polymer poly(oligo(ethylene glycol) methacrylate) in flow-through chromatography mode. The virus-like particles were selectively excluded, while the relatively smaller sized host cell proteins were absorbed. The exclusion of virus-like particles was governed by the accessibility of binding sites (the size of adsorbents and the charge of grafted dextran chains) as well as the architecture (branch-chain length) of the grafted polymer. The branch-chain length of grafted polymer was altered by changing the type of monomers used. The larger adsorbent (90 µm) had an approximately twofold increase in the flow-through recovery, as compared to the smaller adsorbent (30 µm). Generally, polymer-grafted adsorbents improved the exclusion of the virus-like particles. Overall, the middle branch-chain length polymer grafted on larger adsorbent showed optimal performance at 92% flow-through recovery with a purification factor of 1.53. A comparative study between the adsorbent with dextran grafts and the polymer-grafted adsorbent showed that a better exclusion of virus-like particles was achieved with the absorbent grafted with inert polymer. The grafted polymer was also shown to reduce strong interaction between binding sites and virus-like particles, which preserved the particles' structure.

A Holistic Approach to Managing Microalgae for Biofuel Applications.

Microalgae contribute up to 60% of the oxygen content in the Earth's atmosphere by absorbing carbon dioxide and releasing oxygen during photosynthesis. Microalgae are abundantly available in the natural environment, thanks to their ability to survive and grow rapidly under harsh and inhospitable conditions. Microalgal cultivation is environmentally friendly because the microalgal biomass can be utilized for the productions of biofuels, food and feed supplements, pharmaceuticals, nutraceuticals, and cosmetics. The cultivation of microalgal also can complement approaches like carbon dioxide sequestration and bioremediation of wastewaters, thereby addressing the serious environmental concerns. This review focuses on the factors affecting microalgal cultures, techniques adapted to obtain high-density microalgal cultures in photobioreactors, and the conversion of microalgal biomass into biofuels. The applications of microalgae in carbon dioxide sequestration and phycoremediation of wastewater are also discussed.

Metallic and semiconducting carbon nanotubes separation using an aqueous two-phase separation technique: a review.

It is known that carbon nanotubes show desirable physical and chemical properties with a wide array of potential applications. Nonetheless, their potential has been hampered by the difficulties in acquiring high purity, chiral-specific tubes. Considerable advancement has been made in terms of the purification of carbon nanotubes, for instance chemical oxidation, physical separation, and myriad combinations of physical and chemical methods. The aqueous two-phase separation technique has recently been demonstrated to be able to sort carbon nanotubes based on their chirality. The technique requires low cost polymers and salt, and is able to sort the tubes based on their diameter as well as metallicity. In this review, we aim to provide a review that could stimulate innovative thought on the progress of a carbon nanotubes sorting method using the aqueous two-phase separation method, and present possible future work and an outlook that could enhance the methodology.

Thermoseparating aqueous two-phase systems: Recent trends and mechanisms.

Having the benefits of being environmentally friendly, providing a mild environment for bioseparation, and scalability, aqueous two-phase systems (ATPSs) have increasingly caught the attention of industry and researchers for their application in the isolation and recovery of bioproducts. The limitations of conventional ATPSs give rise to the development of temperature-induced ATPSs that have distinctive thermoseparating properties and easy recyclability. This review starts with a brief introduction to thermoseparating ATPSs, including its history, unique characteristics and advantages, and lastly, key factors that influence partitioning. The underlying mechanism of temperature-induced ATPSs is covered together with a summary of recent applications. Thermoseparating ATPSs have been proven as a solution to the demand for economically favorable and environmentally friendly industrial-scale bioextraction and purification techniques.

Investigation of laccase activity in cholinium-based ionic liquids using experimental and molecular dynamics techniques.

Laccases hold great potential for biotechnological applications, particularly in environmental pollutant remediation. Laccase activity is governed by the solvent environment, and ionic liquids (ILs) emerge as a versatile solvent for activation or stabilization of enzymes. Herein, effects of cholinium-based ILs formulated with carboxylic acids, inorganic acid, and amino acids as anionic species, on the catalytic activity of laccase from Trametes versicolor were investigated by experimental and computational approaches. Experimental results showed that laccase activity was enhanced by 21.39 % in 0.5 M cholinium dihydrogen citrate ([Cho][DHC]), in relation to the laccase activity in phosphate buffer medium. However, cholinium aminoate ILs negatively affected laccase activity, as evidenced by the partial deactivation of laccase in both cholinium glycinate and cholinium phenylalaninate, at concentrations of 0.1 M and 0.5 M, respectively. Molecular dynamics studies revealed that the enhancement of laccase activity in [Cho][DHC] might be attributed to the highly stabilized and compact structure of laccase, facilitating a better internal electron transfer during the laccase-substrate interactions. Enhanced catalytic performance of laccase in [Cho][DHC] was postulated to be driven by the high accumulation level of dihydrogen citrate anions around laccase's surface. [Cho][DHC] holds great promise as a cosolvent in laccase-catalyzed biochemical reactions.

Recent advances and challenges in sustainable management of plastic waste using biodegradation approach.

Versatility and desirable attributes of synthetic plastics have greatly contributed towards their wide applications. However, vast accumulation of plastic wastes in environment as a result of their highly recalcitrant nature has given rise to plastic pollution. Existing strategies in alleviating plastic wastes accumulation are inadequate, and there is a pressing need for alternative sustainable approaches in tackling plastic pollution. In this context, plastic biodegradation has emerged as a sustainable and environmental-friendly approach in handling plastic wastes accumulation, due to its milder and less energy-intensive conditions. In recent years, extensive research effort has focused on the identification of microorganisms and enzymes with plastic-degrading abilities. This review aims to provide a timely and holistic view on the current status of plastic biodegradation, focusing on recent breakthroughs and discoveries in this field. Furthermore, current challenges associated to plastic biodegradation are discussed, and the future perspectives for continuous advancement of plastic biodegradation are highlighted.

Enhanced activity of Candida antarctica lipase B in cholinium aminoate ionic liquids: a combined experimental and computational analysis.

As a class of ionic liquids with higher biocompatibility, cholinium aminoates ([Cho][AA]) hold potential as solvation media for enzymatic bioprocessing. Herein, solvation effect of [Cho][AA] on structural stability and enzymatic activity of Candida antarctica lipase B (CALB) was evaluated using experimental and computational approaches. Influence of [Cho][AA] on CALB stability was investigated using amino acid anions ([AA]-) with varying hydrophobicity levels. Choline phenylalaninate ([Cho][Phe]) resulted in 109.1% and 110.4% of relative CALB activity to buffer medium at 25 °C and 50 °C, respectively. Simulation results revealed the improvement of CALB's enzymatic activities by [AA]- with a strong hydrophobic character. Shielding of CALB from water molecules by [AA]- was observed. The level of CALB activity was governed by accumulation level of [AA]- at CALB's first hydration layer. The stronger interaction between His224 and Asp187 was postulated to be driven by [Cho][AA], resulting in the activity enhancement of CALB. The slight improvement of CALB activity in 0.05 M [Cho][Phe] at 50 °C could be due to the larger size of entrance to the catalytic site and the stronger interaction between the catalytic residues. The promising effect of [Cho][Phe] on CALB activation may stimulate research efforts in designing a 'fully green' bioreaction for various industrial applications.Communicated by Ramaswamy H. Sarma.

Effective Low-Powered Photocatalytic Disinfection via Synchronous Introduction of Oxygen Dopants and Carbon Defects in Carbon Nitride.

Establishing an effective metal-free photocatalyst for sustainable applications remains a huge challenge. Herein, we developed ultrathin oxygen-doped g-C3N4 nanosheets with carbon defects (OCvN) photocatalyst via a facile gas bubble template-assisted thermal copolymerization method. A series of OCvN with different dopant amounts ranging from 0 to 10% were synthesized and used as photocatalysts under illumination of low-power (2 × 18 W, 0.18 mW/cm2) and commercially available energy-saving light bulbs. Upon testing for photocatalytic Escherichia coli inactivation, the best-performing sample, OCvN-3, demonstrated an astonishing disinfection activity of over 7-log reduction after 3 h of illumination, boasting an 18-fold improvement in its antibacterial activity compared to that of pristine g-C3N4. The enhanced performance was attributed to the synergistic effects of increased surface area, extended visible light harvesting, improved electronic conductivity, and ultralow resistance to charge transfer. This study successfully introduced a green photocatalyst that demonstrates the most effective disinfection performance ever recorded among metal-free g-C3N4 materials. Its disinfection capabilities are comparable to those of metal-based photocatalysts when they are exposed to low-power light.

Probing the molecular interactions between cholinium-based ionic liquids and insulin aspart: A combined computational and experimental study.

Despite extensive studies revealing the potential of cholinium-based ionic liquids (ILs) in protein stabilization, the nature of interaction between ILs' constituents and protein residues is not well understood. In this work, we used a combined computational and experimental approach to investigate the structural stability of a peptide hormone, insulin aspart (IA), in ILs containing a choline cation [Ch]+ and either dihydrogen phosphate ([Dhp]-) or acetate ([Ace]-) as anions. Although IA remained stable in both 1 M [Ch][Dhp] and 1 M [Ch][Ace], [Dhp]- exhibited a much stronger stabilization effect than [Ace]-. Both the hydrophilic ILs intensely hydrated IA and increased the number of water molecules in IA's solvation shell. Undeterred by the increased number of water molecules, the native state of IA's hydrophobic core was maintained in the presence of ILs. Importantly, our results reveal the importance of IL concentration in the medium which was critical to maintain a steady population of ions in the microenvironment of IA and to counteract the denaturing effect of water molecules. Through molecular docking, we confirm that the anions exert the dominant effect on the structure of IA, while [Ch]+ have the secondary influence. The computational results were validated using spectroscopic analyses (ultra-violet, fluorescence, and circular dichroism) along with dynamic light scattering measurements. The extended stability of IA at 30 °C for 28 days in 1 M [Ch][Dhp] and [Ch][Ace] demonstrated in this study reveals the possibility of stabilizing IA using cholinium-based ILs.

Dual (pH and thermal) stimuli-responsive Pickering emulsion stabilized by chitosan-carrageenan composite microgels.

Formulation of water-in-oil (W/O) Pickering emulsion (PE) for food applications has been largely restricted by the limited choices of food-grade Pickering emulsifiers. In this study, composite microgels made of chitosan and carrageenan were explored as a dual (pH and thermal) stimuli-responsive Pickering emulsifier for the stabilization of W/O PE. The chitosan-carrageenan (CS-CRG) composite microgels not only exhibited pH- and thermo-responsiveness, but also displayed enhanced lipophilicity as compared to the discrete polymers. The stability of the CS-CRG-stabilized W/O PE system (CS-CRG PE) was governed by CS:CRG mass ratio and oil fractions used. The CS-CRG PE remained stable at acidic pH and at temperatures below 40 °C. The instability of CS-CRG composite microgels at alkaline pH and at temperatures above 40 °C rendered the demulsification of CS-CRG PE. This stimuli-responsive W/O PE could unlock new opportunities for the development of stimuli-responsive W/O PE using food-grade materials.

Reactive Green 19 dye-ligand immobilized on the aminated nanofiber membranes for efficient adsorption of lysozyme: Process development and optimization in batch and flow systems.

The performance of lysozyme adsorption by the aminated nanofiber membrane immobilized with Reactive Green 19 (RG19) dyes was evaluated in batch and flow systems. The physicochemical properties of the dye-immobilized nanofiber membrane were characterized. The parameters of batch-mode adsorption of lysozyme (e.g., pH, initial dye concentration, and lysozyme concentration) were optimized using the Taguchi method. In a flow process, the factors influencing the dynamic binding performance for lysozyme adsorption in the chicken egg white (CEW) solution include immobilized dye concentration, adsorption pH value, feed flow rate, and feed CEW concentration. The impact of these operating conditions on the lysozyme purification process was investigated. Under optimal conditions, the recovery yield and purification factor of lysozyme achieved from the one-step adsorption process were 98.52% and 143 folds, respectively. The dye-affinity nanofiber membrane also did not exhibit any significant loss in its binding capacity and purification performance after five consecutive uses.

Microbial biodegradation of recalcitrant synthetic dyes from textile-enriched wastewater by Fusarium oxysporum.

The present study reported the improvement of biological treatment for the removal of recalcitrant dyes including aniline blue, reactive black 5, orange II, and crystal violet in contaminated water. The biodegradation efficiency of Fusarium oxysporum was significantly enhanced by the addition of mediators and by adjusting the biomass density and nutrient composition. A supplementation of 1% glucose in culture medium improved the biodegradation efficiency of aniline blue, reactive black 5, orange II, and crystal violet by 2.24, 1.51, 4.46, and 2.1 folds, respectively. Meanwhile, the addition of mediators to culture medium significantly increased the percentages of total removal for aniline blue, reactive black 5, orange II, and crystal violet, reaching 86.07%, 68.29%, 76.35%, and 95.3%, respectively. Interestingly, the fungal culture supplemented with 1% remazol brilliant blue R boosted the biodegradation up to 97.06%, 89.86%, 91.38%, and 86.67% for aniline blue, reactive black 5, orange II, and crystal violet, respectively. Under optimal culture conditions, the fungal culture could degrade these synthetic dyes concentration up to 104 mg/L. The present study demonstrated that different recalcitrant dye types can be efficiently degraded using microorganism such as F. oxysporum.

Preparation of black cumin seed oil Pickering nanoemulsion with enhanced stability and antioxidant potential using nanocrystalline cellulose from oil palm empty fruit bunch.

The groundbreaking innovation and industrialization are ushering in a new era where technology development is integrated with the sustainability of materials. Over the decade, nanocrystalline cellulose (NCC) obtained from lignocellulosic biomass had created a great value in various aspects. The abundantly available empty fruit bunch (EFB) in the palm oil industry has motivated us to utilize it as a sustainable alternative for the isolation of NCC, which is a worthwhile opportunity to the waste management of EFB. Taking advantage of the shape anisotropy and amphiphilic character, NCC has been demonstrated as a natural stabilizer for oil-in-water emulsion. In this work, preparation of highly stable Pickering nanoemulsion using black cumin seed oil and NCC was attempted. Black cumin seed oil is a class of plant oil with various nutritional and pharmaceutical benefits. However, its poor solubility could substantially lower the therapeutic effect, and thus, requires a delivery system to overcome this limitation. The role of NCC in the formation of stable Pickering nanoemulsion was investigated. The emulsification process was found crucial to the resulting droplet size, whereas NCC contributed critically to its stabilization. The droplet size obtained from ultrasonication and microfluidization was approximately 400 nm, as examined using transmission electron microscopy. The droplet (oil-to-water = 2:8) has long-term stability against creaming and coalescence for more than six months. The nanoemulsion stabilized by NCC could allow a better absorption by the human body, thereby maximizing the potential of black cumin seed oil in the personal care and food industries.

Enhanced structural stability of insulin aspart in cholinium aminoate ionic liquids.

Cholinium aminoates [Ch][AA] have gained tremendous interest as a promising ionic liquid medium for the synthesis and storage of proteins. However, high alkalinity of [Ch][AA] limits its usage with pH-sensitive proteins. Here, we probed the structure, stability, and interactions of a highly unstable therapeutic protein, insulin aspart (IA), in a range of buffered [Ch][AA] (b-[Ch][AA]) using a combination of biophysical tools and in silico pipeline including ultraviolet-visible, fluorescence, and circular dichroism spectroscopies, dynamic light scattering measurements and molecular docking. b-[Ch][AA] used in the study differed in concentrations and their anionic counterparts. We reveal information on ion and residue specific solvent-protein interactions, demonstrating that the structural stability of IA was enhanced by a buffered cholinium prolinate. In comparison to the glycinate and alaninate anions, the hydrophilic prolinate anions established more hydrogen bonds with the residues of IA and provided a less polar environment that favours the preservation of IA in its active monomeric form, opening new opportunities for utilizing [Ch][AA] as storage medium.

Extraction of fucoxanthin from Chaetoceros calcitrans by electropermeabilization-assisted liquid biphasic flotation system.

Electropermeabilization-assisted liquid biphasic flotation (LBF) system is an emerging extraction system facilitated by the adsorptive bubble separation and the electroporation in an aqueous two-phase medium. This integrative extraction system is well suited for the direct recovery of intracellular biocompounds from cells without the needs of discrete steps of mid- or down-stream bioprocessing. The potential of electropermeabilization-assisted LBF system in bioseparation was demonstrated in this study by using the diatom Chaetoceros calcitrans (C. calcitrans) as the source of fucoxanthin, which is a promising antioxidant highly demanded by food and pharmaceutical industries. The extraction performances of LBF and electropermeabilization-assisted LBF system were comprehensively evaluated under the optimal operating conditions. Comparatively, the optimized LBF and electropermeabilization-assisted LBF systems achieved the satisfactory yields of fucoxanthin, i.e., 14.78 mg/g and 16.09 mg/g, respectively. The good recovery of fucoxanthin using electropermeabilization-assisted LBF system could be attributed to the higher release of fucoxanthin from the electrotreated C. calcitrans, allowing a higher partition of fucoxanthin to the top phase of LBF system (236.72 as compared to 152.15 from LBF system). In addition, the fucoxanthin extracted suing both methods exhibit satisfactory antioxidant activities. The application of electropermeabilization-assisted LBF system in the extraction of fucoxanthin is a greener and highly efficient bioprocessing route which can be prospectively extended to other biocompound extraction from microalgal sources.

PERISCOPE-Opt: Machine learning-based prediction of optimal fermentation conditions and yields of recombinant periplasmic protein expressed in Escherichia coli.

Optimization of the fermentation process for recombinant protein production (RPP) is often resource-intensive. Machine learning (ML) approaches are helpful in minimizing the experimentations and find vast applications in RPP. However, these ML-based tools primarily focus on features with respect to amino-acid-sequence, ruling out the influence of fermentation process conditions. The present study combines the features derived from fermentation process conditions with that from amino acid-sequence to construct an ML-based model that predicts the maximal protein yields and the corresponding fermentation conditions for the expression of target recombinant protein in the Escherichia coli periplasm. Two sets of XGBoost classifiers were employed in the first stage to classify the expression levels of the target protein as high (>50 mg/L), medium (between 0.5 and 50 mg/L), or low (<0.5 mg/L). The second-stage framework consisted of three regression models involving support vector machines and random forest to predict the expression yields corresponding to each expression-level-class. Independent tests showed that the predictor achieved an overall average accuracy of 75% and a Pearson coefficient correlation of 0.91 for the correctly classified instances. Therefore, our model offers a reliable substitution of numerous trial-and-error experiments to identify the optimal fermentation conditions and yield for RPP. It is also implemented as an open-access webserver, PERISCOPE-Opt (http://periscope-opt.erc.monash.edu).