Relationships within theRugopharynx delta species complex (Nematoda: Strongyloidea) from Australian marsupials inferred from allozyme electrophoretic data

Relationships between the strongyloid nematodesRugopharynx delta, R. zeta, R. omega, R. longibursaris, R. mawsonae andR. sigma, all from macropodid marsupials, were investigated using allozyme data. The phylogenetic trees derived from the electrophoretic data set were congruent with those of the hosts and were consistent with the hypothesis that the species complex originated in pademelons of the genusThylogale and diversified in rock-wallabies (Petrogale spp.) and scrub wallabies of the subgenusNotamacropus. Host switching is evident only between closely related macropodid taxa.     

Molecular dynamics studies of the human CD4 protein

A dynamical model for an N-terminal fragment of the human CD4 protein has been determined by computer simulation. The protein has been studied both in vacuo and in solution. Data from both simulations agree moderately well with each other and with the crystal structure. All elements of secondary structure were retained during simulation. Point mutation and sequence replacement studies have shown that a loop in CD4, residues 40–52, is involved in binding with gp120, the human immunodeficiency virus surface glycoprotein.^1,2 Our results show that the gp120-binding loop and a few regions which bind to monoclonal antibodies and class II MHC molecules are the most highly motile areas of the protein. These results are consistent with the suggestion that CD4 binds to target molecules by using induced-fit contacts. © 1994 John Wiley & Sons, Inc.     

Host-parasite associations of Eimeria spp. (Apicomplexa:Eimeriidae) in kangaroos and wallabies of the genus Macropus (Marsupialia:Macropodidae)

Faecal samples from 514 kangaroos and wallabies representing 12 species of the genus Macropus were examined for oocysts of Eimeria spp. Six species of Eimeria were redescribed from their type hosts, and on the basis of finding homologous oocysts in the faeces of other Macropus spp., host ranges for these coccidia were extended. Eimeria hestermani Mykytowycz, 1964 is redescribed from M. giganteus (eastern grey kangaroo) and is described from M. fuliginosus (western grey kangaroo), M. rufogriseus (red-necked wallaby), M. dorsalis (black-striped wallaby), and M. eugenii (tammar wallaby). E. toganmainensis Mykytowycz, 1964 is redescribed from M. rufus (red kangaroo) and the host range is extended to M. giganteus, M. fuliginosus, M. rufogriseus and M. eugenii. E. wilcanniensis Mykytowycz, 1964 is redescribed from M. rufus, and the host range is extended to M. giganteus, M. fuliginosus and M. robustus (euro or wallaroo). E. macropodis Wenyon & Scott, 1925 is redescribed from M. rufogriseus, and is described from M. giganteus, M. fuliginosus, M. rufus, M. irma (western brush wallaby), M. parryi (whip-tailed wallaby), M. dorsalis, M. eugenii, and M. parma (parma wallaby). E. fausti Yakimoff & Matschoulsky, 1936, E. cunnamullensis Mykytowycz, 1964 and E. purchasei Mykytowycz, 1964 are synonymized with E. macropodis. E. marsupialium Yakimoff & Matschoulsky, 1936 is redescribed from M. giganteus, and from M. fuliginosus. E. gungahlinensis Mykytowycz, 1964 is redescribed from M. fuliginosus, and from M. giganteus. Seven new species of Eimeria are described. E. flindersi, new species, is described from M. eugenii, M. rufogriseus, and M. antilopinus (antilopine wallaroo). E. prionotemni, new species, is described from M. eugenii, M. parryi, M. rufogriseus, M. agilis (agile wallaby) and M. dorsalis. E. mykytowyczi, new species, is described from M. agilis, M. antilopinus, and M. parryi. E. parryi, new species, is described from M. parryi. E. yathongensis, new species, is described from M. fuliginosus and M. giganteus. E. parma, new species, is described from M. parma, and E. desmaresti, new species, is described from M. rufogriseus. E. kogoni Mykytowycz, 1964, and E. rufusi Prasad, 1960 are considered species inquirendae. The host-parasite associations of these coccidia, and of similar species of Eimeria in other genera of Macropodoid marsupials, are discussed in relation to the postulated phylogeny of the hosts.     

Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.     

Amikacin disrupts the cell envelope of Pseudomonas aeruginosa ATCC 9027

Amikacin, an aminoglycoside known to inhibit protein synthesis, was found to perturb the outer membrane of a sensitive Pseudomonas aeruginosa strain (ATCC 9027). This perturbation was monitored using electron microscopy and biochemical analyses. Following exposure to 20 micrograms amikacin/mL for 15 min, the outer membrane of exponentially growing cells lost 15% of its protein, 18% of its lipopolysaccharide, and 18% of its phosphate. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis showed that the whole spectrum of outer membrane protein and lipopolysaccharide was affected. Similarly, atomic absorption spectrophotometry revealed that magnesium and calcium were also lost. When cells were treated with amikacin, electron microscopy of negative stains showed a substantial increase in outer membrane blebbing. Freeze fractures revealed changes in membrane fracture pattern and particle distribution, and thin sections revealed a sequential disruption of the cell envelope beginning at the outer membrane and ending at the plasma membrane. This study supports the proposal that aminoglycoside antibiotics cross the outer membrane of Pseudomonas aeruginosa by displacing metal cations necessary to stabilize the organic constituents of the membrane. Their removal results in loss of the outer membrane and the formation of transient small holes which permit the antibiotic access to the cytoplasmic membrane where it is transported into the cytoplasm.     

Unusual stability of the Methanospirillum hungatei sheath.

The proteinaceous sheath of Methanospirillum hungatei was isolated by lysing cells in 50 mM dithiothreitol, separating the sheath from other cellular material by discontinuous sucrose density centrifugation, and removing the "cell spacers" with dilute NaOH. The isolated sheath material consisted of hollow tubes which had a highly ordered surface array. The stability of the sheath to treatment with denaturants and to enzymatic digestion was examined by a turbidimetric assay in conjunction with electron microscopy and optical or electron diffraction. The sheath was resistant to a range of proteases and also was not digested by peptidoglycan-degrading enzymes, a lipase, a cellulase, a glucosidase, or Rhozyme (a mixture of galactosidases, acetylglucosaminidase, acetylgalactosaminidase, fucosidase, and mannosidases). In addition to being unaffected by common salts, thiol-reducing agents, and EDTA, the layer was resistant to powerful denaturants such as 6 M urea, 6 M guanidinium hydrochloride, 10 M LiSCN, cyanogen bromide, sodium periodate, and 1% sodium dodecyl sulfate. Strong bases, boiling 3 N HCl, and performic acid did attack the sheath; in these cases, the array was systematically disassembled in a progressive manner, which was followed by electron microscopy. The layer was slightly modified by N-bromosuccinimide in urea, but the array remained intact. The stability of the sheath was remarkable, not only as compared to other bacterial surface arrays, but also as compared to proteins generally, and possibly indicated the presence of covalent cross-links between protein subunits.     

Effect of growth temperature on the morphology and performance ofZymomonas mobilis ATCC 29 191 in batch and continuous culture

Summary Increasing the temperature in chemostat culture ofZymomonas mobilis ATCC 29 191 with low and high glucose concentrations was found to result in a decreasing frequency of septation leading to the formation of long filaments and in increasing outer membrane blebbing. Whether this effect is strain specific or universal inZymomonas is, unknown. Improvements in the fermentation kinetics could be achieved at elevated temperatures, with an optimum at 33°C. Temperatures >30°C induced uncoupled growth in chemostat cultures ofZ. mobilis ATCC 29 191. The results of this study emphasize the importance of temperature regulation in optimizing the performance of continuous fermentations withZymomonas.Nomenclature D Dilution rate, 1/h - _max Maximum specific growth rate, 1/h - S _R Initial substrate concentration, g glucose/1 - S Amount of glucose consumed, g glucose/1 - S ₀ Effluent substrate concentration, g glucose/1 - X Biomass concentration - g cells/1 - [P] Amount of product formed, g ethanol/1 - [P] Product concentrations, g ethanol/l - Y _x/s Growth yield, g cells/g glucose used - Y _p/s Product yield, g ethanol/g glucose used - O _s Specific rate of glucose uptake, g glucose/g cells/h - Q _p Specific rate of ethanol formation, g ethanol/g cells/h - VP Volumetric productivity, g ethanol/1/h - t Fermentation time, h Corresponding author