A SIMPLE METHOD OF DNA EXTRACTION OF MYCOBACTERIUM TUBERCULOSIS FROM SPUTUM CULTURES FOR SEQUENCING ANALYSIS

Background:

Concern has been raised about DNA extraction from Mycobacterium tuberculosis due to its complex procedure. This study demonstrates a simple and fast DNA extraction method of mycobacterial genome to subsequent molecular investigation, such as Polymerization Chain Reaction (PCR) amplification, with species-specific primers and sequencing.

Materials and Methods:

Total DNA was isolated from M. tuberculosis cultured by using boil method. DNA was evaluated via measures of DNA quantity and quality (absorbance at 230, 260 and 280 nm), DNA integrity (electrophoresis). Molecular tests were tested namely PCR and sequencing.

Conclusions:

The quality of DNA obtained is acceptable for PCR and sequencing analysis. These findings demonstrate that the method used is inexpensive and suitable for minimum infrastructure facilities.

A SIMPLE METHOD OF DNA EXTRACTION OF MYCOBACTERIUM TUBERCULOSIS FROM SPUTUM CULTURES FOR SEQUENCING ANALYSIS

Background: Concern has been raised about DNA extraction from Mycobacterium tuberculosis due to its complex procedure. This study demonstrates a simple and fast DNA extraction method of mycobacterial genome to subsequent molecular investigation, such as Polymerization Chain Reaction (PCR) amplification, with species-specific primers and sequencing. Materials and Methods: Total DNA was isolated from M. tuberculosis cultured by using boil method. DNA was evaluated via measures of DNA quantity and quality (absorbance at 230, 260 and 280 nm), DNA integrity (electrophoresis). Molecular tests were tested namely PCR and sequencing. Conclusions: The quality of DNA obtained is acceptable for PCR and sequencing analysis. These findings demonstrate that the method used is inexpensive and suitable for minimum infrastructure facilities.

Gelatin Extraction Optimization from Skin of Sub Adult and Adult Pangasius Hypophthalmus

Fish skin is the potential gelatin source since the increase of the demand for the halal food due to the religious consideration. The yield of gelatin obtained from connective tissue of animal skin greatly affected by the extraction process and age of the animals that used as raw material. Research about the potential of the Pangasius hypophthalmus (striped catfish) skin as halal gelatin source have been developing. However, there was no information about the correlation between the length of striped catfish that representing age with the gelatin content. Here we optimize the gelatin extraction method from striped catfish skin with different length body size (sub adult and adult size) using statistical analysis of Placket Burman Design. We performed preliminary study to determine the variables used in the main study. We used 9 variables in the extraction process and analyzed the p-value of each variable. According to this analysis, three variables with the lowest p-values were selected: temperature (p=0.000); soaking time in alkali solution (p=0.055) and soaking time in acid solution (p=0.244). Range value of selected variables were determined according to the related previous studies. Results from our study showed that the maximum yield of sub adult and adult were obtained when we used 70 °C as temperature of extraction, i.e. 37.42% and 30.31%, respectively. In general, sub adult striped catfish have higher yield than the adult one at the temperature of 40 and 70 °C. However, the gelatin yielded from extraction process temperature of ≥70 °C exhibited dark pigmentation, while the gelatin that obtained with temperature treatment of ≤ 55°C showed less pigmentation. The gelatin yielded from sub adult striped catfish showed more pigmentation than the adult one. We suggested for process of extraction both size of striped catfish should be at 55°C, since it showed higher yield extraction with less pigmentation.

Efect of Gamma 60Co Irradiation on The Growth, Lipid Content and Fatty Acid Composition of Botryococcus sp. Microalgae

<p><em>Botryococcus</em> sp. is one of microalgae species that has a high lipid content as much as 75% of their dry weight. But, lipid production by microalgae is regulated by their environmental condition (pH, light, temperature, nutrition, etc). Mutagenesis induced by Gamma ⁶⁰Co irradiation can be utilized to alter the <em>Botryococcus</em> sp. genetic to get microalgae mutant strain that can produce a higher lipid content than the wild strain. <em>Botryococcus</em> sp. was irradiated with different doses of gamma ray of ⁶⁰Co  (0, 2, 4, 6, and 10 Gy),  and the effect  on the growth, lipid content, and fatty acid composition of microalgae were observed. Research design used is random complete (RAL) with 95 %  confident level for quantitive analysis based on the biomass and lipid contents. More over fatty acid composition was analyzed by Gas Cromatography-Mass Spectrometry<em> </em>(GC-MS). Results showed that Gamma irradiated gave an effect on growth and lipid content of <em>Botryococcus</em> sp. But between the control treatment (0 Gy) with microalgae irradiated dose of 2 Gy, 4 Gy and 6 Gy were not significantly different. Whereas between the control with 10 Gy irradiated was significantly different. The highest biomassa and lipid content are found in 10 Gy irradiated microalgae with 0.833 gram biomass and 41% lipid content. Fatty acid profile of <em>Botryococcus</em> sp. control has 6 fatty acids while 10 Gy irradiated microalgae has 12 fatty acids, with the long-chain fatty acids increased, whereas short-chain fatty acids decreased.</p>

Laccase oxidation and removal of toxicants released during combustion processes

This study reports for the first time the ability of laccases adsorbed on cellulose acetate to eliminate toxicants released during combustion processes. Laccases directly oxidized and eliminated more than 40% w/v of 14 mM of 1,4-dihydroxybenzene (hydroquinone); 2-methyl-1,4-benzenediol (methylhydroquinone); 1,4-dihydroxy-2,3,5-trimethylbenzene (trimethylhydroquinone); 3-methylphenol (m-cresol); 4-methylphenol (p-cresol); 2-methylphenol (o-cresol); 1,3-benzenediol (resorcinol); 1,2-dihydroxybenzene (catechol); 3,4-dihydroxytoluene (4-methylcatechol) and 2-naphthylamine. Further, laccase oxidized 2-naphthylamine, hydroquinone, catechol, methylhydroquinone and methylcatechol were also able to in turn mediate the elimination of >90% w/v of toxicants which are per-se non-laccase substrates such as 3-aminobiphenyl; 4-aminobiphenyl; benz[a]anthracene; 3-(1-nitrosopyrrolidin-2-yl) pyridine (NNN); formaldehyde; 4-(methyl-nitrosamino-1-(3-pyridyl)-1-butanone (NNK); 2-butenal (crotonaldehyde); nitric oxide and vinyl cyanide (acrylonitrile). These studies demonstrate the potential of laccase immobilized on solid supports to remove many structurally different toxicants released during combustion processes. This system has great potential application for in situ removal of toxicants in the manufacturing, food processing and food service industries.

Cellulose oxidation and bleaching processes based on recombinant Myriococcum thermophilum cellobiose dehydrogenase

Myriococcum thermophilum cellobiose dehydrogenase (MtCDH) was expressed in Pichia pastoris using the pPICZαA expression vector under the control of methanol inducible AOX promoter. The purified recombinant MtCDH with a specific activity of 3.1 Umg(-1) was characterized to obtain kinetic constants for various carbohydrate substrates. Additionally, the C1 oxidation of the reducing ends of cellobiose, cellotetraose and maltotriose by MtCDH was verified by HPLC-MS. MtCDH was employed to oxidize several different cellulose-based materials by production of hydrogen peroxide. Based on the obtained results a one-pot enzymatic scouring/bleaching process for cotton fabrics was developed using pectinases as scouring agent and MtCDH to produce H(2)O(2) for bleaching. An average increase in whiteness (Berger) ΔE of 26 and an average 95% increase in wettability were observed in all MtCDH treated fabrics. In addition, MtCDH oxidized typical colored cotton flavonoids (morin, rutin, isoquercitrin).

Enzymatic synthesis of lignin-siloxane hybrid functional polymers

This study combines the properties of siloxanes and lignin polymers to produce hybrid functional polymers that can be used as adhesives, coating materials, and/or multifunctionalized thin-coating films. Lignin-silica hybrid copolymers were synthesized by using a sol-gel process. Laccases from Trametes hirsuta were used to oxidize lignosulphonates to enhance their reactivity towards siloxanes and then were incorporated into siloxane precursors undergoing a sol-gel process. In vitro copolymerization studies using pure lignin monomers with aminosilanes or ethoxytrimethylsilane and analysis by ²⁹Si NMR spectroscopy revealed hybrid products. Except for kraft lignin, an increase in lignin concentration positively affected the tensile strength in all samples. Similarly, the viscosity generally increased in all samples with increasing lignin concentration and also affected the curing time.

Cellular and plasma antioxidant activity assay using tetramethoxy azobismethylene quinone

The kinetics of the reduction of enzymatically generated tetramethoxy azobismethylene quinone (TMAMQ), a newly developed antioxidant activity assay method, by pure cellular and plasma antioxidants was studied. Further, the potential application of TMAMQ to the estimation of the antioxidant activity of clinical serum samples was investigated. The highest reduction rate (k) was obtained with ascorbic acid (1.11x10(-2)microM(-1) s(-1)) and glutathione showed the lowest (2.94x10(-5)microM(-1) s(-1)). Comparing TMAMQ and the commercially available antioxidant method Total Antioxidant Capacity clearly shows a similar trend, although the values differ. This study also shows that TMAMQ is highly sensitive (only a minute plasma sample was required) and reproducible, and the reaction proceeds until steady state (until all antioxidants have reacted). TMAMQ is very stable in acetonitrile (>3months), making it a highly flexible method because it can be easily adapted for analysis of just a single sample or for high-throughput analysis. This has direct implications on reducing costs and experimental steps. TMAMQ is therefore a highly promising antioxidant activity assay method for cellular and plasma antioxidant activity assay.

Polymerization of lignosulfonates by the laccase-HBT (1-hydroxybenzotriazole) system improves dispersibility

The ability of laccases from Trametes villosa (TvL), Myceliophthora thermophila (MtL), Trametes hirsuta (ThL) and Bacillus subtilis (BsL) to improve the dispersion properties of calcium lignosulfonates 398 in the presence of HBT as a mediator was investigated. Size exclusion chromatography showed an extensive increase in molecular weight of the samples incubated with TvL and ThL by 107% and 572% from 28400 Da after 17h of incubation, respectively. Interestingly, FTIR spectroscopy, (13)C NMR and Py-GC/MS analysis of the treated samples suggested no substantial changes in the aromatic signal of the lignosulfonates, a good indication of the ability of TvL/ThL-HBT systems to limit their effect on functional groups without degrading the lignin backbone. Further, the enzymatic treatments led to a general increase in the dispersion properties, indeed a welcome development for its application in polymer blends.

Reactivity of long chain alkylamines to lignin moieties: implications on hydrophobicity of lignocellulose materials

Enzymatic processes provide new perspectives for modification of lignocellulose materials. In the current study, laccase catalyzed coupling of long chain alkylamines to lignin model molecules and lignocellulose was investigated. Up to two molecules of dodecylamine (DA) and dihexylamine (DHA) were successfully coupled with lignin monomers (guaiacol, catechol and ferulic acid) while coupling onto complex lignin model compounds (syringylglycerol beta-guaiacyl ether, guaiacylglycerol beta-guaiacyl ether and dibenzodioxocin) yielded 1:1 coupling products. Surface analysis of beech veneers enzymatically grafted with DA showed an increase in nitrogen content of 3.18% compared to 0.71% in laccase only treated controls while the O/C ratio decreased from 0.52 to 0.46. Concomitantly the grafting of DHA or DA onto beech veneers resulted in a 53.8% and 84.2% increase in hydrophobicity, respectively when compared to simple adsorption. Therefore, laccase-mediated grafting of long chain alkylamines onto lignocellulose materials can be potentially exploited for improving their hydrophobicity.

Laccase catalyzed covalent coupling of fluorophenols increases lignocellulose surface hydrophobicity

This work presents for the first time the mechanistic evidence of a laccase-catalyzed method of covalently grafting hydrophobicity enhancing fluorophenols onto Fagus sylvatica veneers. Coupling of fluorophenols onto complex lignin model compounds guaiacylglycerol beta-guaiacyl ether and syringylglycerol beta-guaiacyl ether was demonstrated by LC-MS and NMR. Laccase-mediated coupling increased binding of 4-[4-(trifluoromethyl)phenoxy]phenol (4,4-F3MPP) and 4-(trifluoromethoxy)phenol (4-F3MP) to veneers by 77.1% and 39.2%, respectively. XPS studies showed that laccase-catalyzed grafting of fluorophenols resulted in a fluorine content of 6.39% for 4,4-F3MPP, 3.01% for 4-F3MP and 0.26% for 4-fluoro-2-methylphenol (4,2-FMP). Grafting of the fluorophenols 4,2-FMP, 4-F3MP and 4,4-F3MPP led to a 9.6%, 28.6% and 65.5% increase in hydrophobicity, respectively, when compared to treatments with the respective fluorophenols in the absence of laccase, in good agreement with XPS data.