Genomic DNA extraction from medicinal plants available in Malaysia using a TriOmic(TM) improved extraction kit

DNA extraction was carried out on 32 medicinal plant samples available in Malaysia using the TriOmic(TM) extraction kit. Amounts of 0.1 g flowers or young leaves were ground with liquid nitrogen, lysed at 65°C in RY1(plus) buffer and followed by RNAse treatment. Then, RY2 buffer was added to the samples and mixed completely by vortexing before removal of cell debris by centrifugation. Supernatants were transferred to fresh microcentrifuge tubes and 0.1 volume RY3 buffer was added to each of the transferred supernatant. The mixtures were applied to spin columns followed by a centrifugation step to remove buffers and other residues. Washing step was carried out twice by applying 70% ethanol to the spin columns. Genomic DNA of the samples was recovered by applying 50 μL TE buffer to the membrane of each spin column, followed by a centrifugation step at room temperature. A modification of the TriOmic(TM) extraction procedure was carried out by adding chloroform:isoamyl alcohol (24:1) steps in the extraction procedure. The genomic DNA extracted from most of the 32 samples showed an increase of total yield when chloroform:isoamyl alcohol (24:1) steps were applied in the TriOmicTM extraction procedure. This preliminary study is very important for molecular studies of medicinal plants available in Malaysia since the DNA extraction can be completed in a shorter period of time (within 1 h) compared to manual extraction, which entails applying phenol, chloroform and ethanol precipitation, and requires 1-2 days to complete.     

Novel solid-phase extraction strategy for the isolation of basic drugs from whole blood Preliminary study using commercially available extraction cartridges

A novel strategy for the solid-phase extraction of basic drugs has been developed using commercial extraction cartridges. The procedure involves the sequential application of very different isolation mechanisms, viz. hydrophobic extraction on non-porous carbon followed by ionic extraction on a strong cation exchanger. This approach to extraction achieves both high recoveries and clean extracts when analysed by GC-MS. The potential for automation has been demonstrated using commercial sample preparation equipment.     

Efficacy of a commercially available post-thaw bovine semen sexing kit in both single-ovulating and hyperstimulated cows

Currently, there are few inexpensive, reliable, effective methods for commercially separating X- and Y-chromosome bearing fresh and frozen bovine sperm. The objective of these experiments was to determine the efficacy of a commercially available post-thaw bovine semen sexing kit, HeiferPlus™ (HP) which claims to alter the sex ratio in favor of female calves following artificial insemination. Three trials included the insemination of hyperstimulated cows with Control or HP-treated semen, non-surgical embryo collection on Day 7, and a combined PCR/dot blot assay to determine embryo sex. Chi-square analysis showed that the Control group produced a greater proportion (p < 0.0005) of female embryos than the HP group. There were no differences in the proportions of transferable compared with degenerate embryos or in number of ovulations, embryos, and unfertilized ova collected from Control compared with HP groups. When treatments were combined, one of the two bulls used in the hyperstimulation studies produced an overall greater proportion of females (p < 0.05), suggesting a bull effect.Another trial involved the insemination of cows synchronized via OvSynch^® with fetal sexing via ultrasonography. Results of these studies indicated that HP semen sexing kit did not alter the sex ratio in favor of females in either hyperstimulated or single-ovulating cows; however, potential bull effects may be further evaluated to understand the capacity of HP with semen from specific bulls. Additionally, perhaps the sex of the surviving embryo can be manipulated by the maternal side, through ovarian, hormonal, oviductal, or uterine influences.     

Improved sample preparation for the testosterone hydroxylation assay using disposable extraction columns

The preparation of samples for injection into a high-performance liquid chromatography from assay mixtures for the determination of cytochrome P-450-dependent testosterone hydroxylation has been substantially facilitated. By replacing the multiple cumbersome extraction steps of the conventional method with a single column extraction the time for sample preparation was reduced from hours to minutes. The new procedure also yields better recoveries for most of the testosterone metabolites than the original protocol. The use of extraction columns for sample preparation allows the simultaneous treatment of a large number of samples or even the automation of the whole assay procedure. The modified procedure is a straightforward, easy-to-perform method that should greatly facilitate the implementation of the testosterone hydroxylation assay for sharply discriminating between many individual cytochrome P-450 species in routine enzyme diagnostics.     

Using a commercial DNA extraction kit to obtain RNA for RT-PCR from starchy rice endosperm

The extraction of RNA from a starchy plant material, such as many common food grains, is difficult, and especially so from the mature endosperm of rice. Most commercial RNA kits are not suitable for starchy materials. Traditional RNA extraction procedures, in addition to being laborious and time consuming, leave hazardous organic wastes that result in expensive disposal costs. Interestingly, the numerous commercial DNA isolation kits now available often include directions for eliminating co-isolated RNA. This indicated an approach to obtain the generally unwanted RNA by-product by treating the total extraction product to intentionally retain RNA. A method was developed by which a two-step DNase procedure was applied to the product of the Cartagen Food DNA extraction kit that eliminated the DNA but left the co-extracted RNA. This modified procedure was compared with several other commercial and standard methods that are promoted as being able to work under high polysaccharide conditions. Successful extraction was determined by the production and amplification of cDNA by RT-PCR of actin. Extraction was successful from milled rice, as well as from cornmeal and wheat flour. The modification provides an RNA extraction method that is quick, easy, and inexpensive, and also eliminates the production of hazardous wastes.     

Column-based method to simultaneously extract DNA, RNA, and proteins from the same sample

We describe a procedure for the simultaneous extraction of proteins and nucleic acids from the same experimental sample allowing for direct correlations between genetic, genomic, and proteomic data. This approach, using commercially available column-based nucleic acid extraction kits, requires no hazardous chemicals and is a quick, reliable, and consistent method for concomitant protein extraction. Buffer choice is critical to completely solubilize all proteins in the sample. Proteins solubilized in radioimmunoprecipitation assay (RIPA) buffer did not represent the entire profile when compared with conventionally extracted proteins using the same buffer at the one-dimensional (1-D) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) level, however proteins extracted from the columns and solubilized in a two-dimensional (2-D) electrophoresis lysis buffer showed a similar profile to conventionally extracted proteins when analyzed at both the 1-D and the 2-D level. We further showed that proteins extracted using these methods were compatible with Western blot analysis. This technique provides a simple and effective way to analyze protein and nucleic acids simultaneously from the same sample without affecting yield and quality.     

Miniaturized solid-phase extraction and sample preparation for MALDI MS using a microfabricated integrated selective enrichment target

A microfabricated proteomic sample preparation and sample presentation device, Integrated Selective Enrichment Target, (ISET), comprising an array of 96 perforated nanovials is described. Each perforated nanovial can be filled with solid-phase extraction media for purification and concentration of peptides prior to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The validity of the ISET sample preparation is shown by analysis of low nM-pM standard samples, as well as biological samples. The ISET solid-phase extraction sample preparation was compared to ZipTip and MassPREP PROtarget sample preparation, demonstrating a superior performance with respect to number of detected peptides and signal intensity of detected peptides.     

Comparison of a bacteriophage-delivered DNA vaccine and a commercially available recombinant protein vaccine against hepatitis B

A bacteriophage lambda DNA vaccine expressing the small surface antigen (HBsAg) of hepatitis B was compared with Engerix B, a commercially available vaccine based on the homologous recombinant protein (r-HBsAg). Rabbits (five per group) were vaccinated intramuscularly at weeks 0, 5 and 10. Antibody responses against r-HBsAg were measured by indirect enzyme-linked immunosorbent assay, by limiting dilutions and by subtyping. Specific lymphocyte proliferation in vitro was also measured. After one vaccination, three of the five phage-vaccinated rabbits showed a strong antibody response, whereas no r-HBsAg-vaccinated animals responded. Following two vaccinations, all phage-vaccinated animals responded and antibody levels remained high throughout the experiment (220 days total). By 2 weeks after the second vaccination, antibody responses were significantly higher (P<0.05) in the phage-vaccinated group in all tests. After three vaccinations, one out of five r-HBsAg-vaccinated rabbit still failed to respond. The recognized correlate of protection against hepatitis B infection is an antibody response against the HBsAg antigen. When combined with the fact that phage vaccines are potentially cheap to produce and stable at a range of temperatures, the results presented here suggest that further studies into the use of phage vaccination against hepatitis B are warranted.     

Degradation of the framework of the Chlamydomonas cell wall by proteases present in a commercially available alpha-amylase preparation

A commercially available alpha-amylase derived from Bacillus licheniformis contained an enzymatic activity able to degrade the inner portion or framework of the cell wall of Chlamydomonas reinhardtii. Both the wall-degrading activity and the contaminating protease were destroyed by heating the alpha-amylase preparation at 90 degrees C for 30 min. Since the alpha-amylase activity was uneffected by heat treatment, we conclude that it was not the alpha-amylase but the contaminating protease in the preparation that was responsible for the cell wall-degrading activity.     

蒙古沙冬青总RNA提取与mRNA分离方法的研究

蒙古沙冬青是分布于我国西北荒漠区的常绿旱生阔叶灌木,因其富含多糖和多酚等次生代谢物质,用常规RNA提取方法难以从中获得高质量总RNA.本研究通过在热酚法的RNA提取液中加入高浓度的KAc和β巯基乙醇,从该植物的不同样品中提取到高质量总RNA,并用筛选到的合适试剂盒分离到高纯度的mRNA.所得到的总RNA和mRNA已被成功应用于基因克隆和SMART全长eDNA文库的构建.     

Degradation of the framework of the Chlamydomonas cell wall by proteases present in a commercially available alpha-amylase preparation.

A commercially available alpha-amylase derived from Bacillus licheniformis contained an enzymatic activity able to degrade the inner portion or framework of the cell wall of Chlamydomonas reinhardtii. Both the wall-degrading activity and the contaminating protease were destroyed by heating the alpha-amylase preparation at 90 degrees C for 30 min. Since the alpha-amylase activity was uneffected by heat treatment, we conclude that it was not the alpha-amylase but the contaminating protease in the preparation that was responsible for the cell wall-degrading activity.     

Isolation and characterization of the proteolytic enzyme component from commercially available crude trypsins

A purification procedure for the isolation of a mixture of the major proteolytic pancreatic enzymes (trypsin, chymotrypsin, and elastase) from commercial crude trypsins is described. These enzymes are apparently the enzymes responsible for tissue dispersal in numerous cell culture systems. Materials toxic to cell cultures, present in certain crude trypsin samples, are removed during a purification involving centrifugation, dialysis, treatment with a cellulose ion-exchange resin, removal of salts, and lyophilization. While the fundamental use of this proteolytic mixture would be to prepare primary cell culture, the broad peptide bond specifleity of this mixture would suggest application in cases where a general protease, free of other enzymatic activities, is required.     

Comparative evaluation of bacteria identification from the Acinetobacter genus using a commercially available API 20NE system, PCR and RFLP techniques

A study was carried out for identification of 50 Acinetobacter strains isolated from various clinical materials. Using classic methods the following species were identifies: Acinetobacter sp. (68%), Acinetobacter baumanii (24%) and Acinetobacter lwofii (8%). In all strains the recA gene was found of 435-500 pz size which confirms their belonging to that genus. Amplification products were digested with restriction enzymes Mbol and HinfI (RFLP) and their detection was carried out on agarose gel by electrophoresis methods, owing to that the arrangement of gene fragment characteristic of each strain was obtained. After careful analysis restriction patterns were obtained corresponding to the following genome species: Acinetobacter baumanii (60%), Acinetobacter sp. 3 (28%) and Acinetobacter lwoffii (12%). The methods of molecular biology made possible a more precise classification of the studied strains according to species. Certain strains determined as Acinetobacter sp. by the API 20NE system were found to be Acinetobacter baumanii, Acinetobacter sp. 3 or Acinetobacter lwofii when determined by the PCR/RFLP method.     

A simple and ultra-low cost homemade seamless ligation cloning extract (SLiCE) as an alternative to a commercially available seamless DNA cloning kit

The seamless ligation cloning extract (SLiCE) method is a novel seamless DNA cloning tool that utilizes homologous recombination activities in Escherichia coli cell lysates to assemble DNA fragments into a vector. Several laboratory E. coli strains can be used as a source for the SLiCE extract; therefore, the SLiCE-method is highly cost-effective.The SLiCE has sufficient cloning ability to support conventional DNA cloning, and can simultaneously incorporate two unpurified DNA fragments into vector. Recently, many seamless DNA cloning kits have become commercially available; these are generally very convenient, but expensive. In this study, we evaluated the cloning efficiencies between a simple and highly cost-effective SLiCE-method and a commercial kit under various molar ratios of insert DNA fragments to vector DNA. This assessment identified that the SLiCE from a laboratory E. coli strain yielded 30?85% of the colony formation rate of a commercially available seamless DNA cloning kit. The cloning efficiencies of both methods were highly effective, exhibiting over 80% success rate under all conditions examined. These results suggest that SLiCE from a laboratory E. coli strain can efficiently function as an effective alternative to commercially available seamless DNA cloning kits.