Genetic markers are now routinely used in a wide range of applications, from forensic DNA analysis to marker-assisted plant and animal breeding. The usual practice in such work is to extract the DNA, prime the markers of interest, and sift them out by electrically driving them through an appropriate matrix, usually a gel. The gels, made from polyacrylamide or agarose, are of high cost, limiting their greater applications in molecular marker work, especially in developing countries where such technology has great potential. Trials using superfine resolution (SFR) agarose for SSR marker screening showed that it is capable of resolving SSR loci and can be reused up to 14 times, thus greatly reducing the cost of each gel run. Furthermore, for certain applications, low concentrations of agarose sufficed and switching to lithium borate buffer, instead of the conventional Tris-borate-ethylenediaminetetraacetic acid buffer, will further save time and cost. The 2.5% gel was prepared following the Agarose SFR(TM) manual by adding 2.5 g agarose powder into 100 mL 1X lithium borate buffer in a 250-mL flask with rapid stirring. Two midigels (105 x 83 mm, 17 wells) or 4 minigels (50 x 83 mm, 8 wells), 4 mm thickness can be prepared from 100 mL gel solution. A total of 1680 PCR products amplified using 140 SSR markers from oil palm DNA samples were tested in this study using SFR recycled gel. As average, the gel can be recycled 8 times with good resolution, but can be recycled up to 14 times before the resolutions get blurred.
Agarose gel electrophoresis is the standard method that is used to separate, identify, and purify DNA fragments. However, this method is time-consuming and capable of separating limited range of fragments. A new technique of gel preparation was developed to improve the DNA fragment analysis via electrophoresis.
A new microextraction procedure termed agarose gel liquid phase microextraction (AG-LPME) combined with gas chromatography-mass spectrometry (GC-MS) was developed for the determination of selected polycyclic aromatic hydrocarbons (PAHs) in water. The technique utilized an agarose gel disc impregnated with the acceptor phase (1-octanol). The extraction procedure was performed by allowing the solvent-impregnated agarose gel disc to tumble freely in the stirred sample solution. After extraction, the agarose gel disc was removed and subjected to centrifugation to disrupt its framework and to release the impregnated solvent, which was subsequently withdrawn and injected into the GC-MS for analysis. Under optimized extraction conditions, the new method offered high enrichment factors (89-177), trace level LODs (9-14ngL(-1)) and efficient extraction with good relative recoveries in the range of 93.3-108.2% for spiked drinking water samples. AG-LPME did not exhibit any problems related to solvent dissolution, and it provided high extraction efficiencies that were comparable to those of hollow fiber liquid phase microextraction (HF-LPME) and significantly higher than those of agarose film liquid phase microextraction (AF-LPME). This technique employed a microextraction format and utilized an environmentally compatible solvent holder that supported the green chemistry concept.
The oxidation of ferrous to ferric ions due to ionizing radiation has been used for chemical dosimetry since 1927. The introduction of metal indicator dye xylenol orange (XO) sensitises the measurement of ferric ion yield. A ferrous sulphate- agarose- xylenol orange (FAX) gel was prepared and the gel then exposed to dose ranging from 0.2 to 10 Gy using various high energy photon and electron beams from a linear accelerator. Some general characteristics of FAX such as energy dependence, optical density (OD)-dose relationship, reproducibility and auto-oxidation of ferrous ions were analysed. The radiation yield G of the gel was calculated for gels prepared in oxygen and in air and the values were 46.3 +/- 2.1 and 40.9 +/- 1.4 Fe3+ per 100 eV for photons respectively. However for stock gel which was kept for 5 days pre-irradiation the G value decreased to 36.6 +/- 1.1. The gel shows linearity in OD-dose relationship, energy independence and reproducibility over the dose range investigated. Auto-oxidation of ferrous ions resulted in optical density changes of less than 1.5% per day.
A new microextraction procedure termed multi-walled carbon nanotube-impregnated agarose film microextraction (MWCNT-AFME) has been developed. The method utilized multi-walled carbon nanotubes (MWCNTs) immobilized in agarose film to serve as adsorbent in solid phase microextraction (SPME). The film was prepared by mixing the MWCNTs in agarose solution and drying the mixture in oven. Extraction of selected polycyclic aromatic hydrocarbons was performed by inserting a needle through circular MWCNT-impregnated agarose films (5 mm diameter) and the assembly was dipped into an agitated sample solution prior to micro high performance liquid chromatography-ultraviolet analysis. Back extraction was then performed using ultrasonication of the films in 100 μL of solvent. The film was discarded after single use, thus avoiding any analyte carry-over effect. Due to the mesoporous nature of the agarose film, the MWCNTs were immobilized easily within the film and thus allowing for close contact between adsorbent and analytes. Under the optimized extraction conditions, the technique achieved trace LODs in the range of 0.1 to 50 ng L(-1) for the targeted analytes, namely fluoranthene, phenanthrene and benzo[a]pyrene. The method was successfully applied to the analysis of spiked green tea beverage samples with good relative recoveries in the range of 91.1 to 107.2%. The results supported the feasibility of agarose to serve as adsorbent holder in SPME which then minimizes the consumption of chemicals and disposal cost of organic wastes.
Agarose-chitosan-immobilized octadecylsilyl-silica (C18) film micro-solid phase extraction (μSPE) was developed and applied for the determination of phenanthrene (PHE) and pyrene (PYR) in chrysanthemum tea samples using high performance liquid chromatography-ultraviolet detection (HPLC-UV). The film of blended agarose and chitosan allows good dispersion of C18, prevents the leaching of C18 during application and enhances the film mechanical stability. Important μSPE parameters were optimized including amount of sorbent loading, extraction time, desorption solvent and desorption time. The matrix match calibration curves showed good linearity (r⩾0.994) over a concentration range of 1-500ppb. Under the optimized conditions, the proposed method showed good limits of detection (0.549-0.673ppb), good analyte recoveries (100.8-105.99%) and good reproducibilities (RSDs⩽13.53%, n=3) with preconcentration factors of 4 and 72 for PHE and PYR, respectively.
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.
Agarose film liquid phase microextraction (AF-LPME) procedure for the extraction and preconcentration of polycyclic aromatic hydrocarbons (PAHs) in water has been investigated. Agarose film was used for the first time as an interface between donor and acceptor phases in liquid phase microextraction which allowed for selective extraction of the analytes prior to gas chromatography-mass spectrometry. Using 1-octanol as acceptor phase, high enrichment factors in the range of 57-106 for the targeted analytes (fluorene, phenanthrene, fluoranthene and pyrene) were achieved. Under the optimum extraction conditions, the method showed good linearity in the range of 0.1-200 μgL(-1), good correlation coefficients in the range of 0.9963-0.9999, acceptable reproducibility (RSD 6.1-9.2%, n=3), low limits of detection (0.01-0.04 μgL(-1)) and satisfactory relative recoveries (92.9-104.7%). As the AF-LPME device was non-expensive, reuse or recycle of the film was not required, thus eliminating the possibility of analytes carry-over between runs. The AF-LPME technique is environment-friendly and compatible with the green chemistry concept as agarose is biodegradable polysaccharide extracted from seaweed and the procedure requires small volume of organic solvent and generates little waste. The validated method was successfully applied to the analysis of the four analytes in river water samples.
Molecularly imprinted silica gel (MISG) was incorporated through dispersion in agarose polymer matrix to form a mixed matrix membrane (MMM) and was applied for the determination of three sulfonamide antibiotic compounds (i.e. sulfamethoxazole (SMX), sulfamonomethoxine (SMM), and sulfadiazine (SDZ)) from environmental water samples. Several important microextraction conditions, such as type of desorption solvent, extraction time, amount of sorbent, sample volume, pH, and effect of desorption time, were comprehensively optimized. A preconcentration factors of ≥ 20 was achieved by the extraction of 12.5 mL of water samples using the developed method. This microextraction-HPLC method demonstrated good linearity (1-500 μg L-1) with a coefficient of determination (R2) of 0.9959-0.9999, low limits of detection (0.06-0.17 μg L-1) and limits of quantification (0.20-0.56 μg L-1), good analyte recoveries (80-96%), and acceptable relative standard deviations (< 10%) under the optimized conditions. The method is systematically compared to those reported in the literature.