DNA isolation protocol for seaweeds

We report a DNA isolation protocol for red seaweeds. Recovering DNA of high quality and quantity is a prerequisite for ensuring suitable applications, such as polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) analysis, and sequencing. Isolation of DNA from seaweeds has proven difficult because of coprecipitation of polysaccharides. Our process minimizes this contamination, which is mostly due to the highly hydrocolloidal content of algal cell walls. This protocol, using 2 steps, is based on a preliminary enzymatic digestion of cell wall with specific enzymes (Novozymes) followed by centrifugation, allowing isolation of DNA on the pellet. This provides a higher yield of DNA, in the range of 40 μg (Palmaria palmata) and 18 μg (Gracilaria verrucosa) from 50 mg of fresh frozen pellet.     

Optimized protocol for the pilot-scale preparation of fungal cellulase

Summary A 25-l scale protocol is devised for the optimal secretion and recovery of fungal cellulase. Using a selected higher yieldingTrichoderma viride SMC strain, a protocol consisted of: a) an optimized production medium rich in microcrystalline cellulose (MCC), fortified with 1% (w/v) ammonium sulphate, 0.5% (w/v) soybean flour, 0.1% (v/v) Tween-80 and other trace nutrients; b) optimized physical parameters of production, such as an inoculum containing a homogeneous suspension of 6×10⁷ conidia per 1,28±1°C, pH 4.0±0.5, 300±20 rpm, 11000±1000 l/h aeration, and 170–220 h duration; c) optimal recovery through a filter press (450 l/h rate of filtration) followed by precipitation with 2.5–3.0 volumes of acetone (15°C and basket centrifugation (27°C, 1700 rpm)); and d) vacuum drying (35°C, 4–6 h). This afforded 70% recovery of cellulase in the form of white fluffy powder containing 20000±2000 carboxy methyl cellulase and 1000±50 units filter paperase per g activities, with raw material cost of US$ 8–10 per million carboxy methyl cellulase units. During storage for 18 months at 4°C, ambient temperature and 37°C, the cellulase preparation was found to retain 100, 75 and 60% of its initial activity, respectively.     

A simple protocol for isolation of fungal DNA

Genomic DNA was isolated from as little as 2 mg dry biomass of Magnaporthe grisea by microwave treatment within 30 s. The quantity of DNA was good enough for PCR analysis and Dot blot hybridization. This technique can be used for various studies, such as DNA fingerprinting to study the population structure of the phytopathogen in different regions, and for a quick screening of M. grisea transformants.     

One-step isolation of neutrophils using an elutriator

Summary To simplify the isolation of neutrophils, we developed a one-step procedure using elutriation. The perfusate (0.2% gelatin and 0.1% glucose in phosphate buffered saline) was pumped through an elutriator rotor at 4 ml/min (25° C) with the rotor speed at 2370 rpm. Twenty milliliters of anticoagulated porcine venous blood were mixed with 60 ml of perfusate and loaded into the elutriator chamber. The flow rate was increased by 2 ml/min increments and 100-ml fractions of effluent were collected at each increment. Concentrations of neutrophils and mononuclear cells were measured in each fraction, and the percentage of total neutrophils or mononuclear cells was plotted against flow rate. The optimal yield (46%) and purity (95.1%) of neutrophils (n=8) was obtained in pooled fractions at flow rates greater than 20 ml/min. Neutrophils in this preparation were round, the granules were intact, and the nuclei were lobulated. In addition, the cells produced superoxide in the presence of phorbol myristate acetate and phagocytosed zymosan particles. These characteristics were similar to those of porcine neutrophils prepared by a conventional sedimentation method. The yield (43%) and purity (94%) of human neutrophils isolated using the elutriator method was similar to that for porcine cells. This one-step method provides a moderate yield of pure neutrophils that have retained their morphology and function. This work was supported by the Canadian Heart Foundation.     

Optimized protocol for efficient transfection of dendritic cells without cell maturation

Dendritic cells (DCs) can be considered sentinels of the immune system which play a critical role in its initiation and response to infection¹. Detection of pathogenic antigen by naïve DCs is through pattern recognition receptors (PRRs) which are able to recognize specific conserved structures referred to as pathogen-associated molecular patterns (PAMPS). Detection of PAMPs by DCs triggers an intracellular signaling cascade resulting in their activation and transformation to mature DCs. This process is typically characterized by production of type 1 interferon along with other proinflammatory cytokines, upregulation of cell surface markers such as MHCII and CD86 and migration of the mature DC to draining lymph nodes, where interaction with T cells initiates the adaptive immune response^2,3. Thus, DCs link the innate and adaptive immune systems. The ability to dissect the molecular networks underlying DC response to various pathogens is crucial to a better understanding of the regulation of these signaling pathways and their induced genes. It should also help facilitate the development of DC-based vaccines against infectious diseases and tumors. However, this line of research has been severely impeded by the difficulty of transfecting primary DCs⁴.Virus transduction methods, such as the lentiviral system, are typically used, but carry many limitations such as complexity and bio-hazardous risk (with the associated costs)^5,6,7,8. Additionally, the delivery of viral gene products increases the immunogenicity of those transduced DCs^9,10,11,12. Electroporation has been used with mixed results^13,14,15, but we are the first to report the use of a high-throughput transfection protocol and conclusively demonstrate its utility.In this report we summarize an optimized commercial protocol for high-throughput transfection of human primary DCs, with limited cell toxicity and an absence of DC maturation¹⁶. Transfection efficiency (of GFP plasmid) and cell viability were more than 50% and 70% respectively. FACS analysis established the absence of increase in expression of the maturation markers CD86 and MHCII in transfected cells, while qRT-PCR demonstrated no upregulation of IFNβ. Using this electroporation protocol, we provide evidence for successful transfection of DCs with siRNA and effective knock down of targeted gene RIG-I, a key viral recognition receptor^16,17, at both the mRNA and protein levels. Download video file.^{(52M, mov)}     

Characterization of surface alloantigens of murine neutrophils

Serological analysis of highly purified (>97%) mouse peritoneal exudate neutrophils using a protein-A rosetting technique, showed that these cells possessed the surface phenotype: Ig^–, Thy-1^–, Ly-1^–, Ly-2^–, Ly-3^–, Ly-4⁺, Ly-5⁺, Ly-6⁺, Ly-7^–, Ia^–, FcR⁺ and C3R⁺.     

DNA isolation protocol for red seaweed (rhodophyta)

We report a DNA isolation protocol for red seaweed. The method is a modification of the Dellaporta et al. (1983) protocol for land plants. Our simplified version can be used to process large sample numbers and to minimise polysaccharide co-isolation. The protocol was applied to 12 red seaweed species as well as one green alga and one land plant. The protocol yields about 5 μg of high molecular weight DNA from 10 mg of dried material, with no RNA. No sign of degradation was observed after agarose gel electrophoresis for both freshly extracted DNA and DNA stored for 18 months at 4°C. DNA isolated by our protocol was suitable for genomic library construction (tested for one species), endonuclease restriction, and PCR amplification for all species.     

An improved protocol for the isolation and cultivation of embryonic mouse myocytes

In vitro cultures of cardiomyocytes have proven to be a useful tool for toxicological, pharmacological, and developmental studies, as well as for the study of the cellular and molecular mechanisms responsible for proper myocyte function. One deficient area of research is that of myocyte proliferation. Cardiomyocyte proliferation dramatically diminishes soon after birth and has a very limited occurrence within the adult heart, thus limiting the use of adult cells for proliferation studies. An improved understanding of the requirements for myocyte proliferation will allow for the development of better approaches to repair damaged heart tissue. Here, we provide a protocol for the reliable isolation of embryonic mouse myocytes. These myocytes behave similarly to those in vivo, including their ability to proliferate, providing an ideal system for the study of cardiomyocyte proliferation.     

Rapid isolation of murine primary hepatocytes for chromosomal analysis

Primary hepatocyte culture is a crucial tool for investigations of liver function and for evaluating the toxic effects of drugs. In addition, chromosomal analysis of hepatocytes could also prove useful for understanding the mechanisms of hepatocarcinogenesis. However, cultivation of primary hepatocytes for chromosome analysis has been hampered by the specific equipment and skill required to perform the in situ perfusion step necessary for isolation of primary hepatocytes. In the present study, we aimed to establish a simple and efficient method of isolating hepatocytes suitable for chromosome analysis. We performed hepatocyte isolation without using collagenase perfusion, instead digesting liver tissues using collagenase in tubes. In addition, we examined hepatocyte and bone marrow cell (BMC) co-culture and cultivation of hepatocytes with medium containing BMC culture medium supernatants. We found that hepatocyte viability and attachment rate were significantly improved, both by co-culture with BMCs and medium containing BMC culture media supernatants, with the latter also significantly increasing the mitotic index. Using this simple method of isolation and cultivation, we could successfully perform chromosomal analysis of mouse primary hepatocytes. This method has the potential to help understand the mechanisms underlying chromosomal instability-mediated hepatocarcinogenesis.     

Simple and rapid protocol for the isolation of PCR-amplifiable DNA from medicinal plants

Medicinal plant species has a valuable economic importance because of its usage as pharmaceuticals, nutritional, as well as its use in popular medication. For DNA-based techniques, nanogram quantities of the purified DNA are requisite to amplify and yield sufficient amounts of PCR products. SDS-based DNA isolation method was used to extract DNA from 11 species of different aromatic and medicinal plants collected from Saudi Arabia. Three hundred milligrams of fresh shredded plant material was necessary. The DNA purity was further confirmed by agarose gel, restriction endonuclease digestion and microsatellite primed-polymerase chain reaction (MP-PCR). DNA yields ranged from 10-20 μg (in 100-μL elution volumes) from all plant material evaluated. The DNA obtained was free of any contaminating proteins, polysaccharides and colored pigments. The extracted genomic DNA was found suitable for restriction digestion and PCR amplification. Our experimental procedure provides an easy, suitable, non-toxic, cheap, and quick process for the amplification of DNA from medical plant tissue.     

A new protocol for isolation of mitochondrial DNA from cotton seedlings

A procedure to isolate mtDNA from cotton seedlings G. hirsutum and G. barbadense has been developed. The new protocol allows for the isolation of cotton mtDNA of high purity, yield and digestibility by restriction endonucleases. The success of the protocol is based on critical adjustments in the ionic strength of the homogenizing medium and washing buffer, the speed of grinding during homogenization, and the methods used for lysis of the mitochondria.     

Magnetic, microplate-format plasmid isolation protocol for high-yield, sequencing-grade DNA

We have developed a rapid, microplate-format plasmid isolation procedure to purify sequencing-grade DNA templates for high-throughput DNA sequencing operations. A modified lysozyme/boiling method is used to produce a plasmid-containing supernatant that is then purified by iron bead capture. After binding, the beads are pelleted in a magnetic field, washed and the DNA eluted in water. The method yields up to 10 micrograms plasmid DNA from a 1-mL overnight culture in a deep-well microplate. The procedure is suitable for large-scale experiments, amenable to automation and does not require expensive reagents or equipment. The entire protocol can be completed in as little as 2 h, and one technician with a 96-well pipetting station can process up to 48 plates per day. This protocol is ideal for any high-throughput operation in which template quantity, quality and reproducibility are of primary importance.     

A simplified protocol for routine total DNA isolation from salmonid fishes

An efficient total DNA isolation protocol, suitable for routine population genetic screening purposes is described. This phenol based extraction can utilize fresh, frozen or ethanol preserved tissues.