Metabolic engineering is defined as improving the cellular activities of an organism by manipulating the metabolic, signal or regulatory network. In silico reaction knockout simulation is one of the techniques applied to analyse the effects of genetic perturbations on metabolite production. Many methods consider growth coupling as the objective function, whereby it searches for mutants that maximise the growth and production rate. However, the final goal is to increase the production rate. Furthermore, they produce one single solution, though in reality, cells do not focus on one objective and they need to consider various different competing objectives. In this work, a method, termed ndsDSAFBA (non-dominated sorting Differential Search Algorithm and Flux Balance Analysis), has been developed to find the reaction knockouts involved in maximising the production rate and growth rate of the mutant, by incorporating Pareto dominance concepts. The proposed ndsDSAFBA method was validated using three genome-scale metabolic models. We obtained a set of non-dominated solutions, with each solution representing a different mutant strain. The results obtained were compared with the single objective optimisation (SOO) and multi-objective optimisation (MOO) methods. The results demonstrate that ndsDSAFBA is better than the other methods in terms of production rate and growth rate.
Metabolic engineering involves the modification and alteration of metabolic pathways to improve the production of desired substance. The modification can be made using in silico gene knockout simulation that is able to predict and analyse the disrupted genes which may enhance the metabolites production. Global optimization algorithms have been widely used for identifying gene knockout strategies. However, their productions were less than theoretical maximum and the algorithms are easily trapped into local optima. These algorithms also require a very large computation time to obtain acceptable results. This is due to the complexity of the metabolic models which are high dimensional and contain thousands of reactions. In this paper, a hybrid algorithm of Cuckoo Search and Minimization of Metabolic Adjustment is proposed to overcome the aforementioned problems. The hybrid algorithm searches for the near-optimal set of gene knockouts that leads to the overproduction of metabolites. Computational experiments on two sets of genome-scale metabolic models demonstrate that the proposed algorithm is better than the previous works in terms of growth rate, Biomass Product Couple Yield, and computation time.
We describe a method to obtain point and dispersion estimates for the energies of jets arising from b quarks produced in proton-proton collisions at an energy of s = 13 TeV at the CERN LHC. The algorithm is trained on a large sample of simulated b jets and validated on data recorded by the CMS detector in 2017 corresponding to an integrated luminosity of 41 fb - 1 . A multivariate regression algorithm based on a deep feed-forward neural network employs jet composition and shape information, and the properties of reconstructed secondary vertices associated with the jet. The results of the algorithm are used to improve the sensitivity of analyses that make use of b jets in the final state, such as the observation of Higgs boson decay to b b ¯ .
Mesenchymal Stem Cells (MSCs) are adult stem cells that are gaining worldwide attention for their multi-potential use in tissue engineering-based regenerative medicine. They can be obtained from numerous sources and one of the excellent sources is the dental tissue, such as Stem cells that are extracted from the Human Exfoliated Deciduous teeth (SHED). SHED are considered ideal due to their inherent characteristics, including the capability to proliferate quickly with minimal oncogenesis risk, multipotency capacity and their ability to suppress the immune system. On top of these positive cell traits, SHED are easily accessible with the patient's safety assured, posing less ethical issues and could also provide a sufficient number of cells for prospective clinical uses. This is primarily attributed to their ability to differentiate into multiple cell linages, including osteoblasts, odontoblasts, neuronal cells, adipocytes, as well as endothelial cells. Albeit SHED having a bright future, there still remains an obstacle to develop reliable experimental techniques to retain the long-term regeneration potential of the stem cells for prospective research and clinical applications. Therefore, this review aims to describe the various isolation, expansion and cryopreservation techniques used by researchers in this stem cell field. Optimization of these techniques is crucial to obtain distinct SHED culture with preserved stem cell properties, which enable more reproducible results that will be the key for further stem cell therapy development.
A Gram-negative, arsenite-resistant psychrotolerant bacterial strain, Yersinia sp. strain SOM-12D3, was isolated from a biofilm sample collected from a lake at Svalbard in the Arctic area. To our knowledge, this is the first study on the ability of acid-treated and untreated, non-living biomass of strain SOM-12D3 to absorb arsenic. We conducted batch experiments at pH 7, with an initial As(III) concentration of 6.5 ppm, at 30 °C with 80 min of contact time. The Langmuir isotherm model fitted the equilibrium data better than Freundlich, and the sorption kinetics of As(III) biosorption followed the pseudo-second-order rate equation well for both types of non-living biomass. The highest biosorption capacity of the acid-treated biomass obtained by the Langmuir model was 159 mg/g. Further, a high recovery efficiency of 96% for As(III) was achieved using 0.1 M HCl within four cycles, which indicated high adsorption/desorption. Fourier transformed infrared (FTIR) demonstrated the involvement of hydroxyl, amide, and amine groups in As(III) biosorption. Field emission scanning electron microscopy-energy dispersive analysis (FESEM-EDAX) indicated the different morphological changes occurring in the cell after acid treatment and arsenic biosorption. Our results highlight the potential of using acid-treated non-living biomass of the psychrotolerant bacterium, Yersinia sp. Strain SOM-12D3 as a new biosorbent to remove As(III) from contaminated waters.
The conventional treatment process of palm oil mill effluent (POME) produces a highly colored effluent. Colored compounds in POME cause reduction in photosynthetic activities, produce carcinogenic by-products in drinking water, chelate with metal ions, and are toxic to aquatic biota. Thus, failure of conventional treatment methods to decolorize POME has become an important problem to be addressed as color has emerged as a critical water quality parameter for many countries such as Malaysia. Aspergillus fumigatus isolated from POME sludge was successfully grown in POME supplemented with glucose. Statistical optimization studies were conducted to evaluate the effects of the types and concentrations of carbon and nitrogen sources, pH, temperature, and size of the inoculum. Characterization of the fungus was performed using scanning electron microscopy, Fourier transform infrared (FTIR) spectroscopy, and Brunauer, Emmet, and Teller surface area analysis. Optimum conditions using response surface methods at pH 5.7, 35 °C, and 0.57 % w/v glucose with 2.5 % v/v inoculum size resulted in a successful removal of 71 % of the color (initial ADMI of 3,260); chemical oxygen demand, 71 %; ammoniacal nitrogen, 35 %; total polyphenolic compounds, 50 %; and lignin, 54 % after 5 days of treatment. The decolorization process was contributed mainly by biosorption involving pseudo-first-order kinetics. FTIR analysis revealed that the presence of hydroxyl, C-H alkane, amide carbonyl, nitro, and amine groups could combine intensively with the colored compounds in POME. This is the first reported work on the application of A. fumigatus for the decolorization of POME. The present investigation suggested that growing cultures of A. fumigatus has potential applications for the decolorization of POME through the biosorption and biodegradation processes.
The Johor Strait has experienced rapid development of various human activities and served as the main marine aquaculture area for the two countries that bordered the strait. Several fish kill incidents in 2014 and 2015 have been confirmed, attributed to the algal blooms of ichthyotoxic dinoflagellates; however, the cause of fish kill events after 2016 was not clarified and the causative organisms remained unknown. To clarify the potential cause of fish kills along the Johor Strait, a 1-year field investigation was conducted with monthly sampling between May 2018 and April 2019. Monthly vertical profiles of physical water parameters (temperature, salinity, and dissolved oxygen levels) were measured in situ at different depths (subsurface, 1 m, 5 m, and 8 m) depending on the ambient depth of the water column at the sampling stations. The spatial-temporal variability of macronutrients and chlorophyll a content was analyzed. Our results showed that high chlorophyll a concentration (up to 48.8 μg/L) and high biomass blooms of Skeletonema, Chaetoceros, Rhizosolenia, and Thalassiosira were observed seasonally at the inner part of the strait. A hypoxic to anoxic dead zone, with the dissolved oxygen levels ranging from 0.19 to 1.7 mg/L, was identified in the inner Johor Strait, covering an estimated area of 10.3 km2. The occurrence of high biomass diatom blooms and formation of the hypoxic-anoxic zone along the inner part Johor Strait were likely the culprits of some fish kill incidents after 2016.
Agricultural wastewater that produces color are of environmental and health concern as colored effluent can produce toxic and carcinogenic by-products. From this study, batch culture optimization using response surface methods indicated that the fungus isolated from the pineapple solid waste, Curvularia clavata was able to decolorize sterile palm oil mill effluent (POME) which is mainly associated with polyphenol and lignin. Results showed successful decolorization of POME up to 80 % (initial ADMI [American Dye Manufacturing Index] of 3,793) with 54 % contributed by biosorption and 46 % by biodegradation after 5 days of treatment. Analysis using HPLC and GC-MS showed the degradation of color causing compound such as 3-methoxyphenyl isothiocynate and the production of new metabolites. Ecotoxicity test indicated that the decolorized effluent is safe for discharge. To determine the longevity of the fungus for a prolonged decolorization period, sequential batch decolorization studies were carried out. The results showed that lignin peroxidase and laccase were the main ligninolytic enzymes involved in the degradation of color. Carboxymethyl cellulase (CMCase) and xylanase activities were also detected suggesting possible roles of the enzymes in promoting growth of the fungus which consequently contributed to improved decolorization of POME. In conclusion, the ability of C. clavata in treating color of POME indicated that C. clavata is of potential use for decolorization and degradation of agricultural wastewater containing polyphenolic compounds.
This study focuses on the biodegradation of recalcitrant, coloured compounds resulting from auto-oxidation of Acid Orange 7 (AO7) in a sequential facultative anaerobic-aerobic treatment system. A novel mixed bacterial culture, BAC-ZS, consisting of Brevibacillus panacihumi strain ZB1, Lysinibacillus fusiformis strain ZB2, and Enterococcus faecalis strain ZL bacteria were isolated from environmental samples. The acclimatisation of the mixed culture was carried out in an AO7 decolourised solution. The acclimatised mixed culture showed 98 % decolourisation within 2 h of facultative anaerobic treatment using yeast extract and glucose as co-substrate. Subsequent aerobic post treatment caused auto-oxidation reaction forming dark coloured compounds that reduced the percentage decolourisation to 73 %. Interestingly, further agitations of the mixed culture in the solution over a period of 48 h significantly decolourise the coloured compounds and increased the decolourisation percentage to 90 %. Analyses of the degradation compounds using UV-visible spectrophotometer, Fourier transform infrared spectroscopy (FTIR) and high performance liquid chromatography (HPLC) showed complete degradation of recalcitrant AO7 by the novel BAC-ZS. Phytotoxicity tests using Cucumis sativus confirmed the dye solution after post aerobic treatment were less toxic compared to the parent dye. The quantitative real-time PCR revealed that E. faecalis strain ZL was the dominant strain in the acclimatised mix culture.
Extensive use of recalcitrant azo dyes in textile and paper industries poses a direct threat to the environment due to the carcinogenicity of their degradation products. The aim of this study was to investigate the efficiency of Curvularia clavata NZ2 in decolorization of azo dyes. The ability of the fungus to decolorize azo dyes can be evaluated as an important outcome as existing effluent treatment is unable to remove the dyes effectively. C. clavata has the ability to decolorize Reactive Black 5 (RB5), Acid Orange 7 (AO7), and Congo Red azo dyes, utilizing these as sole sources of carbon and nitrogen. Ultraviolet-visible (UV-vis) spectroscopy and Fourier infrared spectroscopy (FTIR) analysis of the extracted RB5's metabolites along with desorption tests confirmed that the decolorization process occurred due to degradation and not merely by adsorption. Enzyme activities of extracellular enzymes such as carboxymethylcellulase (CMCase), xylanase, laccase, and manganese peroxidase (MnP) were also detected during the decolorization process. Toxicity expressed as inhibition of germination was reduced significantly in fungal-treated azo dye solution when compared with the control. The cultivation of C. clavata under sequential batch system also recorded a decolorization efficiency of above 90%. The crude enzyme secreted by C. clavata also showed excellent ability to decolorize RB5 solutions with concentrations of 100 ppm (88-92%) and 1000 ppm (70-77%) without redox mediator. This proved that extracellular enzymes produced by C. clavata played a major role in decolorization of RB5.
In this study, the adsorption behavior of azo dye Acid Orange 7 (AO7) from aqueous solution onto macrocomposite (MC) was investigated under various experimental conditions. The adsorbent, MC, which consists of a mixture of zeolite and activated carbon, was found to be effective in removing AO7. The MC were characterized by scanning electron microscopy (SEM), energy dispersive X-ray, point of zero charge, and Brunauer-Emmett-Teller surface area analysis. A series of experiments were performed via batch adsorption technique to examine the effect of the process variables, namely, contact time, initial dye concentration, and solution pH. The dye equilibrium adsorption was investigated, and the equilibrium data were fitted to Langmuir, Freundlich, and Tempkin isotherm models. The Langmuir isotherm model fits the equilibrium data better than the Freundlich isotherm model. For the kinetic study, pseudo-first-order, pseudo-second-order, and intraparticle diffusion model were used to fit the experimental data. The adsorption kinetic was found to be well described by the pseudo-second-order model. Thermodynamic analysis indicated that the adsorption process is a spontaneous and endothermic process. The SEM, Fourier transform infrared spectroscopy, ultraviolet-visible spectral and high performance liquid chromatography analysis were carried out before and after the adsorption process. For the phytotoxicity test, treated AO7 was found to be less toxic. Thus, the study indicated that MC has good potential use as an adsorbent for the removal of azo dye from aqueous solution.
Reactive dyes account for one of the major sources of dye wastes in textile effluent. In this study, decolorization of the monoazo dye, Acid Orange 7 (AO7) by the Enterococcus faecalis strain ZL that isolated from a palm oil mill effluent treatment plant has been investigated. Decolorization efficiency of azo dye is greatly affected by the types of nutrients and the size of inoculum used. In this work, one-factor-at-a-time (method and response surface methodology (RSM) was applied to optimize these operational factors and also to study the combined interaction between them. Analysis of AO7 decolorization was done using Fourier transform infrared (FTIR) spectroscopy, desorption study, UV-Vis spectral analysis, field emission scanning electron microscopy (FESEM), and high performance liquid chromatography (HPLC). The optimum condition via RSM for the color removal of AO7 was found to be as follows: yeast extract, 0.1% w/v, glycerol concentration of 0.1% v/v, and inoculum density of 2.5% v/v at initial dye concentration of 100 mg/L at 37 °C. Decolorization efficiency of 98% was achieved in only 5 h. The kinetic of AO7 decolorization was found to be first order with respect to dye concentration with a k value of 0.87/h. FTIR, desorption study, UV-Vis spectral analysis, FESEM, and HPLC findings indicated that the decolorization of AO7 was mainly due to the biosorption as well as biodegradation of the bacterial cells. In addition, HPLC analyses also showed the formation of sulfanilic acid as a possible degradation product of AO7 under facultative anaerobic condition. This study explored the ability of E. faecalis strain ZL in decolorizing AO7 by biosorption as well as biodegradation process.
Amending polycyclic aromatic hydrocarbon (PAH)-contaminated soils with biochar may be cheaper and environmentally friendly than other forms of organic materials. This has led to numerous studies on the use of biochar to either bind or stimulate the microbial degradation of organic compounds in soils. However, very little or no attention have been paid to the fact that biochars can give simultaneous impact on PAH fate processes, such as volatilization, sorption and biodegradation. In this review, we raised and considered the following questions: How does biochar affect microbes and microbial activities in the soil? What are the effects of adding biochar on sorption of PAHs? What are the effects of adding biochar on degradation of PAHs? What are the factors that we can manipulate in the laboratory to enhance the capability of biochars to degrade PAHs? A triphasic concept of how biochar can give simultaneous impact on PAH fate processes in soils was proposed, which involves rapid PAH sorption into biochar, subsequent desorption and modification of soil physicochemical properties by biochar, which in turn stimulates microbial degradation of the desorbed PAHs. It is anticipated that biochar can give simultaneous impact on PAH fate processes in soils.
This review discusses the application of bacterial nanocellulose (BNC) and modified BNC in treating wastewater containing heavy metals and dye contaminants. It also highlights the challenges and future perspectives of BNC and its composites. Untreated industrial effluents containing toxic heavy metals are systematically discharged into public waters. In particular, lead (Pb), copper (Cu), cadmium (Cd), nickel (Ni), zinc (Zn), and arsenic (As) are very harmful to human health and, in some cases, may lead to death. Several methods such as chemical precipitation, ion exchange, membrane filtration, coagulation, and Fenton oxidation are used to remove these heavy metals from the environment. However, these methods involve the use of numerous chemicals whilst producing high amount of toxic sludge. Meanwhile, the development of the adsorption-based technique has provided an alternative way of treating wastewater using BNC. Bacterial nanocellulose requires less energy for purification and has higher purity than plant cellulose. In general, the optimum growth parameters are crucial in BNC production. Even though native BNC can be used for the removal of heavy metals and dyes, the incorporation of other materials, such as polyethyleneimine, graphene oxide, calcium carbonate and polydopamine can improve sorption efficiencies.
Genes involved in the 4-aminobenzenesulfonate (4-ABS) degradation pathway of Hydrogenophaga sp. PBC were identified using transposon mutagenesis. The screening of 10,000 mutants for incomplete 4-ABS biotransformation identified four mutants with single transposon insertion. Genes with insertions that impaired the ability to utilize 4-ABS for growth included (1) 4-sulfocatechol 1,2-dioxygenase β-subunit (pcaH2) and 3-sulfomuconate cycloisomerase involved in the modified β-ketoadipate pathway; (2) 4-aminobenzenesulfonate 3,4-dioxygenase component (sadA) involved in aromatic ring hydroxylation; and (3) transposase gene homolog with a putative cis-diol dehydrogenase gene located downstream. The pcaH2 mutant strain accumulated brown metabolite during growth on 4-ABS which was identified as 4-sulfocatechol through thin layer chromatography and HPLC analyses. Supplementation of wild-type sadA gene in trans restored the 4-ABS degradation ability of the sadA mutant, thus supporting the annotation of its disrupted gene.
The stem bark of Calophyllum depressinervosum and Calophyllum buxifolium were extracted and examined for their antioxidant activities, together with cytotoxicity towards human cancer cells. The methanol extract of C. depressinervosum exhibited good DPPH and NO scavenging effects. The strongest BCB inhibition and FIC effects were shown by dichloromethane and ethyl acetate extracts of both species. Overall, DPPH, FRAP and FIC assays showed strong correlation with TPC. For cytotoxicity, hexane extract of C. depressinervosum possessed the strongest anti-proliferative activities towards SNU-1 cells while the hexane extract of C. buxifolium showed the strongest activity towards LS-174T and K562 cells with the IC50 values ranging from 7 to 17 μg/mL. The purification of plant extracts afforded eight xanthones, ananixanthone (1), caloxanthone B (2), caloxanthone I (3), caloxanthone J (4) xanthochymone B (5), thwaitesixanthone (6), 1,3,5,6-tetrahydroxyxanthone (7) and dombakinaxanthone (8). All the xanthones, except 1 were reported for the first time from both Calophyllum species. The xanthones were examined for their cytotoxic effect against K562 leukemic cells. Compounds 1 and 2 showed strong cytotoxicity with the IC50 values of 2.96 and 1.23 μg/mL, respectively. The molecular binding interaction of 2 was further investigated by performing molecular docking study with promising protein receptor Src kinase.
Robertkochia solimangrovi is a proposed marine bacterium isolated from mangrove soil. So far, the study of this bacterium is limited to taxonomy only. In this report, we performed a genomic analysis of R. solimangrovi that revealed its lignocellulose degrading ability. Genome mining of R. solimangrovi revealed a total of 87 lignocellulose degrading enzymes. These enzymes include cellulases (GH3, GH5, GH9 and GH30), xylanases (GH5, GH10, GH43, GH51, GH67, and GH115), mannanases (GH2, GH26, GH27 and GH113) and xyloglucanases (GH2, GH5, GH16, GH29, GH31 and GH95). Most of the lignocellulolytic enzymes encoded in R. solimangrovi were absent in the genome of Robertkochia marina, the closest member from the same genus. Furthermore, current work also demonstrated the ability of R. solimangrovi to produce lignocellulolytic enzymes to deconstruct oil palm empty fruit bunch (EFB), a lignocellulosic waste found abundantly in palm oil industry. The metabolic pathway taken by R. solimangrovi to transport and process the reducing sugars after the action of lignocellulolytic enzymes on EFB was also inferred based on genomic data. Collectively, genomic analysis coupled with experimental studies elucidated R. solimangrovi to serve as a promising candidate in seawater based-biorefinery industry.
Microbacterium sp. strain SZ1 isolated from gold ores of a Malaysia gold mine was found to be highly resistant to arsenic. Here, we report the draft genome sequence of SZ1, which may provide further insights into understanding its arsenic resistance mechanism. In this draft genome, a complete set of ars operons and two additional scattered ars genes were encoded.
The high alkaline condition of concrete naturally protects embedded steel bars from corrosion by forming a passive protective film. The pH of concrete is generally high, but concrete with different mix compositions may have various pH values. The pH of concrete may decrease over time due to long-term mechanical, chemical, biological and physical factors. Therefore, monitoring the pH value of concrete is crucial to checking if its alkalinity is within an acceptable range and ensuring that the concrete structure is in good health condition. However, the pH measurement for cement-based materials is not standardised. Ex-situ leaching, one of the recommended methods for pH measurement, is simple and practical. In this method, the sample will be crushed, leached and tested using a pH electrode probe. The lifespan of the pH electrode probe may decrease due to the existing suspended particles in the solution. Therefore, one recommendation is to filter the solution before using the probe. In this study, the effect of different filtering setups on the pH value of a cement mortar with a cement-to-sand ratio of 1:3 was evaluated. pH test results showed that filtering can produce similar outcomes to those without filtering, regardless of the type of filter paper and its pore size. However, filtering is strongly recommended for electrode protection of the pH meter. As an innovative filtering setup for cement-based materials, syringe filtering was introduced in this study because it is more economical and its operation is simpler compared to the other methods.
Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments.