A refocused and optimized HNCA: Increased sensitivity and resolution in large macromolecules

Summary A 3D optimized, refocused HNCA experiment is described. It is demonstrated to yield a dramatic increase in sensitivity when applied to [¹³C,¹⁵N]-labeled human carbonic anhydrase II, a 29-kDa protein. The reasons for the gain in sensitivity are discussed, and 3 distinct areas for further development are indicated.     

Strain evolution in Caenorhabditis elegans: Transposable elements as markers of interstrain evolutionary history

Evolutionary relationships across taxa can be deduced from sequence divergence of proteins, RNA, or DNA; sequences which diverge rapidly, such as those of mitochondrial genes, have been especially useful for comparisons of closely related species, and-within limits—of strains within a species. We have utilized the transposable element Tcl as a polymorphic marker to evaluate the evolutionary relationships among nine Caenorhabditis elegans strains. For five low-Tcl-copy strains, we compared patterns of restriction fragments hybridizing to a cloned Tc1 probe. Twenty of the 40 Tc1 insertion sites thus characterized were common to all five strains, and so presumably preceded strain divergence; the 20 differential bands were used to construct a maximum-parsimony tree relating these strains. In four high-copy-number stocks (three wild-type strains and a subline), we determined occupancy of 35 individual Tc1 insertion sites by a polymerase chain reaction assay. Surprisingly, the high-copy strains share a common subset of these Tc1 insertions, and the chromosomal distribution of conserved Tc 1 sites is clustered with respect to the other elements tested. These data imply a close evolutionary relationship among the high-copy strains, such that two of these strains appear to have been derived from the highest-copy-number lineage (represented by two stocks) through crossing with a low-Tc1 strain. Abundances of Tc1 elements were also estimated for the four high-copy-number stocks, at 200–500 copies per haploid genome, by quantitative dot-blot hybridization relative to two low-copy strains. Annealing with ³²P-labeled probes corresponding to full-length Tc1, an oligonucleotide within the Tc1 terminal inverted repeats, and an internal Tc1 oligonucleotide, gave essentially identical results—indicating that Tc1 termini exist in the genome primarily as components of full-length Tc1 elements. A composite evolutionary tree is proposed, based on the locations and numbers of Tc1 elements in these strains, which is consistent with a four-branch intraspecific tree deduced previously by maximum-parsimony analyses of mitochondrial sequence changes; it also serves to elucidate the evolutionary history of transposon mobility. Correspondence to: R.J. Shmookler Reis     

Triple resonance HNCCCH experiments for correlating exchangeable and nonexchangeable cytidine and uridine base protons in RNA

Summary A set of triple resonance experiments is presented, providing through-bond H₂N/HN to H6 connectivities in uridines and cytidines in ¹³C-/¹⁵N-labeled RNAs. These connectivities provide an important link between the sequential assignment pathways for the exchangeable and nonexchangeable proton resonances in nucleic acids. Both 2D and pseudo-3D HNCCCH experiments were applied to a 30-nucleotide lead-dependent ribozyme, known as the leadzyme. The HN to H6 connectivities for three uridines in the leadzyme were identified from one 2D H(NCCC)H experiment, and the H₂N to H6 connectivities were identified for seven of the eight cytidines from the combination of a 2D H(NCCC)H and a pseudo-3D H(NCC)CH experiment.     

Serotyping of Adenoviruses Using Immune Electron Microscopy

Immune electron microscopy may be used to determine the type specificity of several common human adenoviruses. The method described utilized equine antisera and was used to serotype adenoviruses within hours after typical cytopathic effect was observed in tissue culture. Adenovirus types 1, 2, 3, 5, 7a, 8, and 11 were isolated from clinical specimens and serotyped by serum neutralization and immune electron microscopy. Five of the seven types were identified consistently and identically by the two methods. Types 7a and 11 were indistinguishable by immune electron microscopy.     

Campylobacter fetus Subspecies jejuni (Vibrio fetus) from Commercially Processed Poultry

Three isolates of the human and animal pathogen Campylobacter fetus ss. jejuni (Vibrio fetus) were obtained from 165 poultry meat samples purchased from local retail stores.     

Evaluation of Accuracy of Multitest Micromethod System for Identification of Enterobacteriaceae

The Analytab system of 20 biochemical tests for identification of Enterobacteriaceae was evaluated in parallel with conventional tests on 128 Enterobacteriaceae, 5 Aeromonas, and 1 Yersinia enterocolitica. The results of tests for H(2)S and indole production, citrate utilization, lysine and ornithine decarboxylase, arginine dihydrolase, nitrate reduction, beta-galactosidase, and fermentation of arabinose, rhamnose, mannitol, and glucose showed almost complete agreement between the two systems. Eighty-eight per cent of Enterobacteriaceae were correctly speciated with the Analytab system; on repeat testing with heavier inocula of organisms failing to ferment glucose initially, the proportion of Enterobacteriaceae correctly speciated became 93%.     

Characterization of Micrococcaceae Isolated from Clinical Sources

The characterization of 556 Micrococcaceae isolates from various clinical sources has been presented. The incidence of coagulase-negative mannitol-positive staphylococci was 3.2% and that of coagulase-positive mannitol-negative staphylococci was 1.6%. There appears to be insufficient justification for the routine reporting of staphylococcal variants from a general bacteriology laboratory, and biotyping should be reserved for special circumstances.     

Wound-healing motility in the green alga Ernodesmis: calcium ions and metabolic energy are required

Wounding a giant cell of the marine alga Ernodesmis verticillata (Kützing) Børgesen (Chlorophyta) induces two concomitant motility phenomena: longitudinal contraction of the protoplasm away from the wound site, and centripetal contraction of the cut end around the central vacuole. Healing is complete within 30 min of wounding. Mechanical extrusion of the protoplasm into the medium with a teasing needle is followed by contraction of the protoplasm into numerous spherical protoplasts within 60 min. Utilizing a simple defined medium, it is shown that motility is almost completely inhibited by the absence of exogenous free Ca²⁺, with 5.0 mM ethylene glycol bis-(-aminoethyl ether)-N,N,N,N-tetraacetic acid present. This inhibition is reversible by rinsing the cells with Ca²⁺-containing medium. Similarly, extruded cytoplasm fails to exhibit motility in Ca²⁺-free medium. The threshold concentration of exogenous free Ca²⁺ is approx. 10^-7 M for wound-induced contraction. The ions Ba²⁺, Cd²⁺ and Sr²⁺ will substitute for Ca²⁺, but the rate of contraction is one-half that with Ca²⁺ present. Although darkness has no inhibitory effect, lower temperature (15°C), cyanide, or micromolar amounts of phosphorylation uncouplers reversibly slow protoplasmic motility in wounded cells and extruded cytoplasm. Carbonylcyanide m-chlorophenylhydrazone and carbonylcyanide p-trifluoromethoxyphenylhydrazone are especially potent inhibitors. These results indicate that cellular wound healing utilizes metabolic energy and requires exogenous free Ca²⁺, implying that motility in Ernodesmis is a true contractile process. Since 1.0 mM La³⁺ completely and reversibly prevents contraction, it is postulated that Ca²⁺ fluxes may actually trigger motility.Abbreviations CCCP carbonylcyanide m-chlorophenylhydrazone - DMSO dimethylsulfoxide - DNP 2,4-dinitrophenol - EGTA ethylene glycol bis-(-aminoethyl ether)-N,N,N,N-tetraacetic acid - FCCP carbonylcyanide p-trifluoromethoxyphenylhydrazone