A simplified biochemistry for DNA sequencing

A simplified method of DNA sequencing by dideoxy chain termination is developed that approaches a single-step protocol. Utilizing the sequencing advantages contributed by a thermophilic polymerase and a guanine analog, stable sequencing reaction concentrates have been obtained that readily perform the entire sequencing reaction simply by adding prepared DNA to each of the four reaction concentrates required by this method. The mechanics and dynamics of these reactions have been investigated and the capacity of these reactions to withstand normal user variation is demonstrated. This study focuses on one form of this simplified method embodied in the FASTaq DNA sequencing kit.     

A simplified intrathymic injection technique for mice

Intrathymic injection is a common technique used for research concerning immunotolerance induction, gene therapy and T cell development in mice. Traditionally used protocols involve major surgery that exposes the thoracic cavity, which results in injury to the mice and increased risk of poor recovery and postsurgical complications such as infection. We introduce a simplified intrathymic injection technique that does not expose the thoracic cavity and virtually eliminates pain, distress and postoperative complications while maintaining high injection efficiency. The technique is suitable for both adult and neonatal mice.     

A simplified protocol for apoptosis assay by DNA content analysis

Apoptotic cells possess specific morphological and biochemical markers. Various methods have been developed to detect apoptosis based on these markers. One of the most common is the fragmentation of genomic DNA. In addition to electrophoresis for the identification of the characteristic 200 base pair ladders and terminal deoxyribonucleotidyltransferase-mediated dUTP-biotin nick end-labeling, DNA content analysis is often employed. This technique is based on the fact that permeablized apoptotic cells release fragmented DNA, resulting in DNA content that is less than that in live diploid cells. Although widely used, we have found that the number of apoptotic cells detected by DNA content analysis is often lower than that detected by other methods. We have developed a simplified version of the flow cytometry-based protocol that detects a number of apoptotic cells closer to that detected by other methods, and which requires a dramatically reduced number of cells. In addition, this simplified protocol allows preparation of a large number of samples at the same time.     

A simplified technique for low temperature methyl methacrylate embedding

A simplified method for low temperature methyl methacrylate embedding with inhibited methyl methacrylate monomer is demonstrated using proper concentrations of benzoyl peroxide and N,N-dimethylaniline. The polymerized tissue blocks cut well and the tissue sections obtained show excellent acid phosphatase activity when demonstrated with the newly improved technique and Goldner's staining. Likewise, double tetracycline labels are well revealed by fluorescence microscopy.     

A simplified technique for producing an ischemic wound model

One major obstacle in current diabetic wound research is a lack of an ischemic wound model that can be safely used in diabetic animals. Drugs that work well in non-ischemic wounds may not work in human diabetic wounds because vasculopathy is one major factor that hinders healing of these wounds. We published an article in 2007 describing a rabbit ear ischemic wound model created by a minimally invasive surgical technique. Since then, we have further simplified the procedure for easier operation. On one ear, three small skin incisions were made on the vascular pedicles, 1-2 cm from the ear base. The central artery was ligated and cut along with the nerve. The whole cranial bundle was cut and ligated, leaving only the caudal branch intact. A circumferential subcutaneous tunnel was made through the incisions, to cut subcutaneous tissues, muscles, nerves, and small vessels. The other ear was used as a non-ischemic control. Four wounds were made on the ventral side of each ear. This technique produces 4 ischemic wounds and 4 non-ischemic wounds in one animal for paired comparisons. After surgery, the ischemic ear was cool and cyanotic, and showed reduced movement and a lack of pulse in the ear artery. Skin temperature of the ischemic ear was 1-10 °C lower than that on the normal ear and this difference was maintained for more than one month. Ear tissue high-energy phosphate contents were lower in the ischemic ear than the control ear. Wound healing times were longer in the ischemic ear than in the non-ischemic ear when the same treatment was used. The technique has now been used on more than 80 rabbits in which 23 were diabetic (diabetes time ranging from 2 weeks to 2 years). No single rabbit has developed any surgical complications such as bleeding, infection, or rupture in the skin incisions. The model has many advantages, such as little skin disruption, longer ischemic time, and higher success rate, when compared to many other models. It can be safely used in animals with reduced resistance, and can also be modified to meet different testing requirements.     

A simplified protocol for preparing DNA from filamentous cyanobacteria

The preparation of good quality genomic DNA from microalgae and plants is often time-consuming because of the need to remove contaminants that may interfere with the downstream enzymatic manipulation of the DNA. Simpler protocols have been reported but these are applicable only to a few species and in many cases are not effective for removing trace contaminants. In this report, we describe a modification of existing protocols that significantly simplified the preparation of genomic DNA from cyanobacteria and plants. A key step in our protocol is the precipitation of DNA in a high concentration of salt (2–2.5 M NaCl) in the presence of isopropanol, immediately following phenol and chloroform extractions. The preparation and enzymatic digestion of the DNA can be performed in a single day. The DNA was easily digested in 2 h at normal restriction enzyme concentrations, and is highly suitable for PCR and Southern hybridization. We successfully used this simplified protocol to prepare genomic DNA from several filamentous cyanobacteria, such asAnabaena sp. PCC 7120,Anabaena siamensis, andSpirulina strains M2 and Kenya. This protocol may also be useful for preparing genomic DNA from other algae and from higher plants.     

Embryonic stem cell lines derived from blastocysts by a simplified technique

We have isolated euploid, pluripotent stem cell lines directly from mouse blastocysts by a simple culture technique. Our method permits cell lines to be derived from individual embryos, without the use of ovariectomy, immunosurgery and conditioned medium. We cultured individual intact blastocysts in MicroTest plates on top of a feeder layer of lethally irradiated STO mouse fibroblasts in a 10-microliters volume of Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FCS). The cell lines maintain a stable complement of 40 chromosomes, form embryoid bodies and differentiate both in culture and in solid tumors.     

A simplified telemetry system for monitoring body temperature in small animals

An inexpensive but reliable telemetry system for long-term, sequential monitoring of body temperature in up to 20 laboratory animals is described. The system consists of frequency-modulated (FM) temperature transmitters, remote-controlled power switches to extend battery life, a multi-channel telemetry receiver, and a frequency counter interfaced with a personal computer to record data. Analysis of body temperature data obtained from four New Zealand White rabbits confirms the reliability and value of this system.     

A simplified screening test for the diagnosis of allergy.

The Quidel allergy screen is a relatively rapid (less than 2 hours) multiallergen dipstick method for detecting specific immunoglobin E antibodies in serum. It was developed to answer the need of primary physician nonspecialists in allergy for a convenient in-office screening test for diagnosing allergy. The new test was evaluated against the benchmark diagnostic skin tests and the radioallergosorbent serologic tests for sensitivity, specificity, accuracy, and technical feasibility in an office setting. It was found that while the Quidel allergy screen lacks the specificity of the standard tests, its overall sensitivity, as defined by the percentage of patients with positive skin reactions who also tested positive with the Quidel screen (68%), its ease of use, and its rapidity warrant its consideration as a screening tool for confirming a possible case of allergy.     

A novel simplified ultra-rapid freezing technique for cryopreservation of tissue slices

Cryopreservation offers the potential to maximize the use and availability of biological materials that have a limited supply. This study demonstrates an enhanced technique for the parallel cryopreservation of a series of liver tissue slices using a tray modeled from aluminium foil and low concentrations of a cryoprotectant. Cooling and warming rates of approximately 2000 and 3900 degrees C min(-1), respectively, were achieved as the thermal capacity of the foil-tray was significantly reduced compared to the aluminium sandwich device introduced by Day et al. [S.H. Day, D.A. Nicoll-Griffith, J.M. Silva, Cryopreservation of rat and human liver slices by rapid freezing, Cryobiology 38 (1999) 154-159]. Additionally, the two critical steps involved in the sandwich approach, i.e., clamping the plates and complete filling of the entire space between the plates with liquid, can be omitted using the foil tray. The viability of the slices was verified by measuring tetrazolium salt reduction capacity, cytosolic enzyme lactate dehydrogenase leakage, and ethoxycoumarin metabolism.     

A simplified universal genomic DNA extraction protocol suitable for PCR

Conventional genomic DNA extraction protocols need expensive and hazardous reagents for decontamination of phenolic compounds from the extracts and are only suited for certain types of tissue. We developed a simple, time-saving and cost-efficient method for genomic DNA extraction from various types of organisms, using relatively innocuous reagents. The protocol employs a single purification step to remove contaminating compounds, using a silica column and a non-hazardous buffer, and a chaotropic-detergent lysing solution that hydrolyzes RNA and allows the selective precipitation of DNA from cell lysates. We used this system to extract genomic DNA from different tissues of various organisms, including algae (Dunaliella salina), human peripheral blood, mouse liver, Escherichia coli, and Chinese hamster ovary cells. Mean DNA yields were 20-30 μg/cm(3) from fresh tissues (comparable to yields given by commercial extraction kits), and the 260/280 nm absorbance ratio was 1.8-2.0, demonstrating a good degree of purity. The extracted DNA was successfully used in PCR, restriction enzyme digestion and for recombinant selection studies.