Shear thickening of DNA in SDS lysates.

Cells of Escherichia coli were subjected to lysis by an alkali detergent treatment (sodium dodecyl sulphate). The rate of detergent lysis was not first order. The rheological properties of the lysate were measured using a controlled stress rheometer. Detergent-lysed cells produced a lysate which showed marked non-Newtonian properties. The material showed a shear thickening at specific low shear stress conditions. The acceleration of the cone during the ascent stage of a flow curve, influenced the shape of the flow curves. These findings are discussed in relation to the form of bacterial DNA in solution.     

Meiotic cytology of Saccharomyces cerevisiae in protoplast lysates

Summary This report describes cytological features of meiosis in Saccharomyces cerevisiae prepared for electron microscopy by lysis of protoplasts or nuclei on an aqueous surface. Whereas the chromatin of cells lysed before or after meiotic prophase was widely dispersed, pachytene bivalents appeared as discrete, elongate masses of compact chromatin. These bivalents were of nearly uniform thickness; they ranged in length from about 0.6 m to 4.0 m, with a median of 1.6–1.8 m. Enzymatic digestion of chromosomal DNA removed the chromatin to reveal the underlying synaptonemal complex. The lysis of partially purified nuclei was less disruptive and thereby revealed the regular association of the telomeres with fragments of the nuclear envelope. In tetraploid cells, pachytene lysates contained quadrivalents characterized by the close apposition of chromatin masses of similar length. One or more points of intimate association appear to represent sites of exchange between pairing partners. The departure of the diploid cells from pachytene was accompanied by the renewed association of spindle microtubules with the chromosomes shortly before the diplotene chromosomes decondensed. Later, the successive meiotic divisions were identified by the appearance of a single spindle for meiosis I and of two spindles for meiosis II.     

High-throughput screening of cell lysates for ganglioside synthesis

A high-throughput screen to detect the synthesis of natural and non-natural gangliosides by cell lysates has been developed and automated. Utilizing the binding specificity of cholera toxin B-subunit for the oligosaccharide moiety of the ganglioside G_M1, the synthesis of sugar–sphingolipid glycosidic linkages was detected using a modified enzyme-linked immunosorbent assay (ELISA)/enzyme-linked lectin assay (ELLA). The screen was optimized and validated for high-throughput screening of cell lysates by evaluating different vectors, promoters, substrates and detection strategies. The extent of ganglioside synthesis was found to be proportional to enzyme concentration and length of incubation time. As a test of the finalized screen efficacy, individual colonies from a saturation mutagenesis library of nucleophile mutants of an endoglycoceramidase were screened to identify the most active enzyme for ganglioside synthesis. This screen should find general application in assaying both glycolipid biosynthesis and glycolipid hydrolysis, as it is highly sensitive and can be used with crude cell extracts.     

Genomic DNA analysis from mouse toe lysates

The protocol described in this report provides a simple, accurate and efficient assay for detection of transgenes and mutations in large colonies of rodents, using crude lysates prepared from the digit cut from the animals for identification purposes. This can be done as early as 6 days of age, minimizing trauma to the mice and allowing assays to be completed long before weaning. Editor's note: The US Food and Drug Administration (FDA) had amended its regulations on good laboratory practice (GLP) for nonclinical laboratory studies regarding humane procedures for animal identification and expreimentation (Vol. 54 # 75). While discouraging use of toe clipping for animal identification, the FDA charged each facility's Institutional Animal Care and Use Committee (IACUC) with the responsibility for evaluation and final approval. C.A.P.     

Multiplex PCR for screening of integrons in bacterial lysates

Bacterial integrons are a useful PCR amplification target in epidemiological surveys of bacterial antibiotic resistance, and a variety of primers have been published. We describe multiplex PCR methodology to test for classes 1, 2 and 3 integron-associated integrases in boiled lysates of Gram-negative bacteria. We report on performance in Acinetobacter spp. (n=50), Enterobacteriaceae (n=76), Pseudomonas aeruginosa (n=15), Bacteroidesspp. (n=69), and in undifferentiated mixed cultures derived from perineal swabs (n=50) and endotracheal aspirates (n=8). This method achieved 100% sensitivity and specificity in simple lysates made from a range of bacteria, without requiring DNA extraction, and is recommended as an efficient screening tool for surveys of integron cassettes.     

Protein microarrays using liquid phase fractionation of cell lysates

We describe an approach in which protein microarrays are produced using a two-dimensional (2-D) liquid phase fractionation of cell lysates. The method involves a pI-based fractionation using chromatofocusing in the first dimension followed by nonporous reversed-phase high-performance liquid chromatography (HPLC) of each pI fraction in the second dimension. This allows fractionation of cellular proteins in the liquid phase that could then be arrayed on nitrocellulose slides and used to study humoral response in cancer. Protein microarrays have been used to identify potential serum biomarkers for prostate cancer. It is shown that specific fractions are immunoreactive against prostate cancer serum but not against serum from healthy individuals. These proteins could serve as sero-diagnostic markers for prostate cancer. Importantly, this method allows for use of post-translationally modified proteins as baits for detection of humoral response. Proteins eliciting an immune response are identified using the molecular mass and peptide sequence data obtained using mass spectrometric analysis of the liquid fractions. The fractionation of proteins in the liquid phase make this method amenable to automation.