A rapid and reliable procedure for extraction of cellular polyamines and inorganic ions from plant tissues

A fast and reliable method for the extraction of cellular polyamines and major inorganic ions (Ca, Mg, Mn, K, and P) from several plant tissues is described. The method involves repeated freezing and thawing of samples instead of homogenization. The efficiency of extraction of both the polyamines and inorganic ions by these two methods was compared for 10 different tissues. In each case, the freeze-thaw procedure resulted in a precise and quantitatively equal, or greater, yield than homogenization. Freeze-thawing not only eliminates the need for various tissue homogenizers (such as polytrons, tissumizers, and mortars and pestles), but it is so simple that a large number of samples can be processed simultaneously. We routinely processed 50–80 samples for quantitation of polyamines and inorganic ions. Freeze-thawing was equally useful for the extraction of polyamines from liver, spleen, and kidney tissues of mice.New Hampshire Agricultural Experiment Station, scientific contribution no. 1845.     

Measurement of plasma unbound unconjugated bilirubin

A method is described for measuring the unconjugated fraction of the unbound bilirubin concentration in plasma by combining the peroxidase method for determining unbound bilirubin with a diazo method for measuring conjugated and unconjugated bilirubin. The accuracy of the unbound bilirubin determination is improved by decreasing sample dilution, eliminating interference by conjugated bilirubin, monitoring changes in bilirubin concentration using diazo derivatives, and correcting for rate-limiting dissociation of bilirubin from albumin. The unbound unconjugated bilirubin concentration by the combined method in plasma from 20 jaundiced newborns was significantly greater than and poorly correlated with the unbound bilirubin determined by the existing peroxidase method (r = 0.7), possibly due to differences in sample dilution between the methods. The unbound unconjugated bilirubin was an unpredictable fraction of the unbound bilirubin in plasma samples from patients with similar total bilirubin concentrations but varying levels of conjugated bilirubin. A bilirubin-binding competitor was readily detected at a sample dilution typically used for the combined test but not at the dilution used for the existing peroxidase method. The combined method is ideally suited to measuring unbound unconjugated bilirubin in jaundiced human newborns or animal models of kernicterus.     

Rapid Isolation And Purification Of Mitochondria For Transplantation By Tissue Dissociation And Differential Filtration

Previously described mitochondrial isolation methods using differential centrifugation and/or Ficoll gradient centrifugation require 60 to 100 min to complete. We describe a method for the rapid isolation of mitochondria from mammalian biopsies using a commercial tissue dissociator and differential filtration. In this protocol, manual homogenization is replaced with the tissue dissociator’s standardized homogenization cycle. This allows for uniform and consistent homogenization of tissue that is not easily achieved with manual homogenization. Following tissue dissociation, the homogenate is filtered through nylon mesh filters, which eliminate repetitive centrifugation steps. As a result, mitochondrial isolation can be performed in less than 30 min. This isolation protocol yields approximately 2 x 10¹⁰ viable and respiration competent mitochondria from 0.18 ± 0.04 g (wet weight) tissue sample.     

A new approach to microhomogenization

A versatile microhomogenizer is described which is capable of handling sample volumes ranging from 1 μl to several millititers. The sample and homogenization buffer are sealed within a segment of flexible plastic tubing. The sample is disrupted by rubbing or rolling a metal rod back and forth over the length of tubing. Centrifugation of the homogenate is performed in the same sealed tubing segment. This method can be used to homogenize single cells.     

Analysis of urinary 3-methoxy-4-hydroxyphenylglycol by high-performance liquid chromatography and electrochemical detection

A high-performance liquid chromatographic method with electrochemical detection for the quantitation of total 3-methoxy-4-hydroxyphenylglycol (MHPG) in human urine is described. Existing methods for deconjugation and extraction have been optimized. The present method is simpler than existing methods with a high precision. Urinary MHPG is deconjugated enzymatically and subsequently extracted with ethyl acetate. The organic layer is extracted with acetic acid and a sample of the aqueous layer is injected into a reversed-phase column. In one run 90 samples can be processed. The critical parameters of deconjugation, extraction and chromatography are described. Data for reproducibility and selectivity are presented.     

Combustion of organic samples by infrared furnace for carbon isotope analysis

An apparatus for converting organic samples to carbon dioxide is described. It is especially designed to determine stable carbon isotope ratio of field samples. Unlike previous apparatus of similar configuration, a "Craig-line," it is free from the deposition of charred carbon on the line that results from an incomplete conversion. It includes an infrared furnace that heats both a CuO column and a sample tube. A removable, stainless-steel tube is present around the heated area, and this particular configuration makes it possible to begin every combustion procedure from room temperature, and consequently, to achieve a complete evacuation of air from the line even for heat-labile samples. The apparatus also includes a column that eliminates contaminating oxides such as nitrous oxide. The time necessary to process a sample is less than 30 min, and the precision of the carbon isotope measurement is comparable with that of "Craig-line." The coefficient of variation of carbon content determinations was no more than a few percents for most samples examined. An incidental finding was made that an isotopic fractionation of uric acid occurred during its preparation from penguin excreta by a high-performance liquid chromatography.     

Comparison of rapid methods for the extraction of bacterial DNA from colonic and caecal lumen contents of the pig

AIMS: The increasing uses of DNA methodologies to study the micro flora of the pig gastrointestinal tract requires an efficient recovery of bacterial DNA from the intestinal sample. Thus, the objective of this study was to determine which DNA extraction methods are most effective for luminal samples from pigs. Several routinely used nucleic acid extraction procedures were compared based upon quantity and purity of extracted DNA. METHODS AND RESULTS: DNA was extracted from pig colonic and caecal lumen samples using 19 methods for bacterial DNA extraction. The quantity of total DNA recovered by each extraction method was determined and compared. Two methods using extraction with polyvinylpolypyrrolidone (PVPP) or phenol and two methods involving bead mill homogenization were found to provide the greatest quantity of extracted DNA for both colonic and caecal lumen. Extracted DNA from these four methods was further analysed for purity based upon the presence of PCR inhibitors, which was ascertained by determining the efficiency of amplification of a segment of the 16S rDNA. PCR amplification could be readily achieved with DNA extracted by each of these four methods, but efficiency of amplification tended to be higher with DNA from two of the methods (one extracted with PVPP and one with bead mill homogenization). CONCLUSIONS: Four extraction methods proved to be significantly superior in quantity of DNA extracted from luminal samples. Of these four, no strong inhibitors of PCR amplification were detected in any of the extracted DNA. However, the efficiency of amplification tended to be lower in DNA samples from two of the methods, suggesting the presence of low levels of PCR inhibitors. SIGNIFICANCE AND IMPACT OF THE STUDY: Results of this study provide a basis for choosing which DNA extraction procedures are most effective for use with samples of pig lumen.     

A new method of sample application for horizontal slab polyacrylamide gel electrophoresis

A new method of sample application for horizontal slab polyacrylamide gel electrophoresis has been developed which solves the main problems associated with existing systems. A quick, simple procedure is described for placing a dry powder mixture of Celite and Sephadex into sample wells of any shape cut to the full depth of the gel slab. Samples can then be added to the powder to form a moist firm bed of material in the wells which prevents leakage of sample from the well. The method enables the quantitative electrophoresis of many samples with widely differing concentrations and volumes without the problems of electrodecantation, loss of electrical contact through the wells, or uneven penetration of sample through the full thickness of the gel.     

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the “gold standard” enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples.     

A rapid,single leaf assay for detecting the presence of ‘S’-male-sterile cytoplasm in maize

Summary A simple, rapid, and reproducible assay is described for determining unambiguously the presence of S-type cytoplasm in male-sterile and male-fertile (restored) maize lines. Because the assay requires only 0.5 g leaf segment per sample, it is a single plant assay and the plant is not destroyed. Plants at any developmental stage can be used. The assay involves a 30 sec homogenization, 20 min centrifugation, one hour lysis, overnight agarose electrophoresis, 30 min gel staining, and photography of the gel to produce a result in much less than 24 hr. Many samples can be assayed simultaneously. The various assay methods available for classifying maize cytoplasms are compared and discussed.     

Cultured human keratinocytes for optical transmission measurement

The challenges of measuring optical properties of human tissues include the thickness of the sample, homogenization, or crystallization from freezing of the tissue. This investigation demonstrates a method to avoid these problems by growing optically thin samples of human keratinocytes as a substitute for ex vivo epidermis samples. Several methods of growth were investigated. Resulting samples were measured on a spectrophotometer for transmission between 300 nm and 2600 nm. The efficacy of the cell growth was confirmed with histological examination of several cultured keratinocyte samples. Limitations were the requirement to measure samples immediately after removal from the incubation environment, and the absence of the irregular structures of normal skin such as hair and glands. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A computer programme for the calculation of radioactivity data from liquid-scintillation counters fitted with external standards

1. A method for transferring data from liquid-scintillation counters to automatic punched-card read-out is described. 2. A method of calibration of an external standard is presented that supplies sufficient information for the correction of quenched data by computer. 3. A computer programme in FORTRAN IV is described that calculates the data from one isotope, or two isotopes counted simultaneously, and that incorporates features for examining the reproducibility of the input data. 4. With the methods described, quench correction of samples containing either (3)H or (14)C was accurate until samples were quenched 70%. When the two isotopes were both present in one sample and counted simultaneously, the correction was accurate until the samples were quenched 60%. When quenching was greater than either 70 or 60% respectively, its correction was still possible but with slightly diminished accuracy and with greater variability.     

Joint inference of population assignment and demographic history

A new approach to assigning individuals to populations using genetic data is described. Most existing methods work by maximizing Hardy-Weinberg and linkage equilibrium within populations, neither of which will apply for many demographic histories. By including a demographic model, within a likelihood framework based on coalescent theory, we can jointly study demographic history and population assignment. Genealogies and population assignments are sampled from a posterior distribution using a general isolation-with-migration model for multiple populations. A measure of partition distance between assignments facilitates not only the summary of a posterior sample of assignments, but also the estimation of the posterior density for the demographic history. It is shown that joint estimates of assignment and demographic history are possible, including estimation of population phylogeny for samples from three populations. The new method is compared to results of a widely used assignment method, using simulated and published empirical data sets.     

Protein estimation in tissues containing high levels of lipid: modifications to Lowry's method of protein determination

A method to estimate protein in detergent-solubilized homogenates of lipid-rich biological samples (e.g., adipose tissue, myelin-enriched fractions of sheep brain) is described. The method is also suitable for samples in which protein is present as a protein-detergent complex. The method involves homogenization of tissue in the presence of a suitable detergent and KCl. Protein is then estimated in an aliquot of this homogenate by Lowry's method in the presence of excess sodium dodecyl sulfate, the solutions being clarified by extraction with ethyl acetate. Protein solubilization by Triton X-100 from adipose tissue was biphasic, extracting two to three times more protein under optimum conditions [1.7 +/- 0.1% (v/v) Triton X-100 and 0.75 M KCl], compared with homogenization without salt and detergent. Unlike adipose tissue, protein solubilization from myelin-enriched fractions of sheep brain peaked at 1% (v/v) Triton X-100, resulting in the extraction of approximately three times more protein than homogenization in the absence of detergent and salt.     

Use of metal chelate affinity chromatography and membrane-based ion-exchange as clean-up procedure for trace residue analysis of tetracyclines in animal tissues and egg

A new and efficient procedure for the clean-up of tetracycline residues in animal tissues and egg prior to reversed-phase high-performance liquid chromatography is described. The principal steps involve homogenization of the tissues in sodium succinate buffer and methanol, followed by centrifugation and clean-up with metal chelate affinity chromatography (MCAC). After further concentration on an Empore extraction membrane with cation-exchange properties, the sample is analysed by HPLC with fluorescence detection. The method was tested on porcine kidney and muscle, bovine liver and whole chicken's egg. The recoveries were determined from spiked tissues for oxytetracycline, tetracycline, chlortetracycline and doxycycline and ranged from 40 to 70%, with repeatabilities below 10% R.S.D.. The analytical responses were linear in the range up to at least 1000 ng/g. The detection limits of the method were estimated at 0.42 ng/g of oxytetracycline, 0.49 ng/g of tetracycline, 0.66 ng/g of chlortetracycline and 1.38 ng/g of doxycycline in porcine muscle, using signal-to-noise ratios of 4:1. Similar detection limits were estimated for kidney, liver and egg. The measured limits of quantification were 2 ng/g for oxytetracycline, 3 ng/g for tetracycline, 4 ng/g for chlortetracycline and 5 ng/g for doxycycline in porcine kidney. The advantage of this method over existing methods is its increased limit of detection.     

A sensitive and convenient method for lipoprotein profile analysis of individual mouse plasma samples

A simple and convenient method to determine plasma cholesterol profiles in individual mouse plasma samples is not presently available. With commonly used methods, plasma samples from several animals in a study group must often be pooled and analyzed, usually by the fast phase liquid chromatography (FPLC) method. The Column Lipoprotein Profile (or CLiP) method described here is a modification of the FPLC method that provides a simple and convenient procedure for determining plasma lipoprotein cholesterol profiles in small sample volumes, allowing determination of profiles from individual animals rather than from pooled plasma. The CLiP method is reproducible; a human sample measured five times over several days produced coefficients of variation as follows: VLDL, 10.0%; LDL, 0.93%; and HDL, 2.51%. CLiP-derived total cholesterol values of five different human samples (with total cholesterol levels ranging from 198 to 263 mg/dL) differed from VAP-II by -1.88% +/- 2.57%. Linearity of differing concentrations for each of the lipoprotein classes was determined by measuring the same sample with different aliquot sizes. The linear regression from VLDL had an r value of 0.996, while LDL, HDL, and total cholesterol all had r values of greater than 0.999. We present a direct comparison of plasma cholesterol profiles from several mouse models with gene modification or expression of transgenic proteins.In conclusion, the CLiP method provides a simple, reliable, and reproducible procedure for determination of plasma cholesterol profiles from individual plasma samples with very low sample volumes, using readily available equipment and reagents.     

Drill-assisted genomic DNA extraction from <Emphasis Type="Italic">Botrytis cinerea</Emphasis>

Current DNA extraction protocols for genomic DNA from Botrytis cinerea almost always start with mycelium that has been reduced to powder with liquid N₂ in a mortar, and this makes their application to a large number of samples slow and cumbersome. Here we present an adaptation of an existing method [Möller et al. (1992) Nucleic Acids Res 20: 6115–6116] for which the initial steps have been modified, including the homogenization of the fungus with sand and the aid of a common household drill. This method allows the processing of large number of samples in much shorter times and generates an average of 4 μg DNA per sample, of sufficient quality for use in PCR and Southern blotting.     

A microplate assay for DNA damage determination (fast micromethod).

A rapid and convenient procedure for DNA damage determination in cell suspensions and solid tissues on single microplates was developed. The procedure is based on the ability of commercially available fluorochromes to interact preferentially with dsDNA in the presence of ssDNA, RNA, and proteins at high pH (>12.0), thus allowing direct measurements of DNA denaturation without sample handling or stepwise DNA separations. The method includes a simple and rapid 40-min sample lysis in the presence of EDTA, SDS, and high urea concentration at pH 10, followed by time-dependent DNA denaturation at pH 12.4 after NaOH addition. The time course and the extent of DNA denaturation is followed in a microplate fluorescence reader at room temperature for less than 1 h. The method requires only 30 ng DNA per single well and could conveniently be used whenever fast analysis of DNA integrity in small samples has to be done, e.g., in patients' lymphocytes after irradiation or chemotherapy (about 3000 cells per sample), in solid tissues or biopsies after homogenization (about 25 microg tissue per well), or in environmental samples for genotoxicity assessment.     

A Microplate Assay for DNA Damage Determination (Fast Micromethod)in Cell Suspensions and Solid Tissues

A rapid and convenient procedure for DNA damage determination in cell suspensions and solid tissues on single microplates was developed. The procedure is based on the ability of commercially available fluorochromes to interact preferentially with dsDNA in the presence of ssDNA, RNA, and proteins at high pH (>12.0), thus allowing direct measurements of DNA denaturation without sample handling or stepwise DNA separations. The method includes a simple and rapid 40-min sample lysis in the presence of EDTA, SDS, and high urea concentration at pH 10, followed by time-dependent DNA denaturation at pH 12.4 after NaOH addition. The time course and the extent of DNA denaturation is followed in a microplate fluorescence reader at room temperature for less than 1 h. The method requires only 30 ng DNA per single well and could conveniently be used whenever fast analysis of DNA integrity in small samples has to be done, e.g., in patients' lymphocytes after irradiation or chemotherapy (about 3000 cells per sample), in solid tissues or biopsies after homogenization (about 25 μg tissue per well), or in environmental samples for genotoxicity assessment.