Rapid determination of vapA/vapB genotype in Rhodococcus equi using a differential polymerase chain reaction method

Rhodococcus equi is a facultative pathogen of foals. Infection causes an often fatal pulmonary pneumonia. The organism has also been isolated from pigs, cattle, humans and the environment. Equine virulence has a high positive correlation with the expression of a 17.4 kD polypeptide of unknown function, VapA, the product of the plasmid-encoded vapA gene. More recently an isogene of vapA, referred to as vapB and encoding an 18.2 kDa polypeptide, has been identified among pig and human isolates. The two genes share > 80% sequence identity, yet their host strains apparently exhibit different pathogenicity profiles (for example by reference to virulence in mouse model system and host specificity). In this study, a polymerase chain reaction (PCR) technique was developed that permits the selective amplification of vapA and vapB. Using this technique the distribution of the two genes among 35 randomly selected isolates of Rhodococcus equi from various animal and environmental sources was determined. Using this technique the genotype of each isolate could be unambiguously assigned as vapA+, vapB+ or vap- (i.e., scoring negative for both vapA and vapB). No isolate scored positive for both vapA and vapB. 100% of equine isolates scored vapA+, confirming the status of vapA as a reliable marker of equine virulence. All three genotypes were found among human isolates; porcine isolates scored either vapB+ or vap- and no vapA+ isolates were present in this sample. Rigorous statistical analysis using the Fisher Exact test confirmed that the high frequency of vapA+ among equine isolates is significant; however the sample size was too small to draw statistically significant conclusions regarding the distribution of genotypes among within other animal groups.     

Oligonucleotide site directed mutagenesis of all histidine residues within the T4 endonuclease V gene: role in enzyme-nontarget DNA binding

In order to evaluate the contributions that histidine residues might play both in the catalytic activities of endonuclease V and in binding to nontarget DNA, the technique of oligonucleotide site directed mutagenesis was used to create mutations at each of the four histidine residues in the endonuclease V gene. Although none of the histidines were shown to be absolutely required for the pyrimidine dimer specific DNA glycosylase activity or the apurinic lyase activity, conservative amino acid changes at His16 produced enzymes with little or no catalytic activity. In addition, the evaluation of conservative and radical amino acid substitutions at positions 34, 56, and 107 is consistent with the interpretation that each of these histidines may be involved in nontarget DNA binding. The data supporting this conclusion are that histidine changes to lysine at positions 34 and 107 enhance the nontarget DNA binding activity of the mutant enzymes while neutralization of charge at His56 reduces nontarget DNA binding.     

PMCA2 mutation causes structural changes in the auditory system in deafwaddler mice

Homozygous deafwaddler mice (dfw/dfw) have a mutation in the gene encoding plasma membrane Ca²⁺ATPase isoform 2 (Pmca2). They walk with a hesitant and wobbly gait, display head bobbing and are deaf. Light microscopy and transmission electron microscopy were used to evaluate the nature and relationship of morphological changes in the cochlea, spiral ganglion cells and spherical cells of the cochlear nucleus in homozygous and heterozygous mice of different ages and controls. Ultrastructural findings showed that in 7 week old homozygous (dfw) mice, inner hair cells and their afferent terminals were present although outer hair cells appeared apoptotic. Stereocilia were absent from the second and third rows of outer hair cells. Ganglion cells were also present although abnormal in appearance. In older homozygous mutants there was a loss of hair cells and spiral ganglion cells. Remaining ganglion cells in this group contained very few cytoplasmic organelles apart from a few hypertrophied mitochondria. In the anteroventral cochlear nucleus, spherical cell soma size was smaller in all homozygous (dfw) mutants than in heterozygous mice and controls. The ultrastructural appearance of the end bulbs of Held in homozygous mutants was abnormal compared with controls, and in the younger group were seen to be swollen, with less distinct synaptic densities and containing large numbers of small synaptic vesicles arranged in clumps. In the older group these synapses were distorted and contained hypertrophied mitochondria and no synaptic densities could be seen, suggesting that these synapses may be non-functional. This study has shown that in homozygous (dfw) mice structural abnormalities occurred not only in cochlear hair cells but also in the spiral ganglion neurones and spherical cells in the cochlear nucleus. It seems likely that these changes are the result of the Pmca2 mutation and the subsequent accumulation of toxic levels of calcium that may lead to alterations in their functional integrity.     

Gramicidin channels: a new mechanism for transmembrane transfer of ions (from high resolution x-ray structural studies of the antibiotic)]

The crystal structure of the membrane-active antibiotic-cyclopeptide gramicidin S complex with urea was determined by the X-ray structure analysis. The gramicidin S molecule possesses an antiparallel beta-structure, its slightly twisted 30-membered cycle has a roughly rectangular form about 4.8 x 13.6 A in size, with the lesser side being formed by the main chain atoms of Phe and Pro residues. The maximum size of the molecule is 22.9 A. A characteristic feature of the molecule is the position of the extended side chains of the Orn residues on one side of the molecular cycle in the form of peculiar "legs--tentacles". One of these legs is "fastened" by the intramolecular H-bond to O atom of the nearer Phe4 residue, the other being free. The distance between the terminal NE atoms of the Orn residues is 5.7 A. The side chains of the Phe and Orn2 residues have trans-orientation, those of the Val, Orn7, Leu residues gauche-orientation. For Val1 and Leu3 side chains statistical disorder of the terminal C atoms is realized. The pyrrolidine rings of the Pro residues adopt Cs-C beta-exo conformation. There are one urea and 20 water molecules per one antibiotic molecule in the structure. The positions of three water molecules are fully occupied, the others with the probability of 0.56-0.20. One of the "water" positions is occupied on 2/3 by water, and on 1/3 by the O atom of the alcohol. There is a complicated system of intra- and intermolecular H-bonds in the structure, with and without the participation of water, alcohol and urea molecules. The gramicidin S molecules, collecting around 3(1) axis according to the left-handed double helix, form the channels whose outside hydrophobic surface is built of the side uncharged radicals, the inside surface being built of the main chain atoms, mainly of the O and N atoms and of the ornithine "tails" with uncharged NE atoms at the termini. The outer diameter of the channel is 29-43 A, inner (without ornithine "tails") is about 12.7 A. At the expense of the change of these "tails" conformation, the inner diameter of the channel filled with water molecules may change from 3.4 up to 6.3 A. Thus, the ions and particles of a rather large size may pass through the channel. The gramicidin channels are discovered and described for the first time. The channels in the crystal structure are close-packed under the hexagonal law.(ABSTRACT TRUNCATED AT 400 WORDS)     

Crustacean zooplankton species richness and associations in reservoirs and ponds of Aguascalientes State, Mexico

We report the species of crustacean zooplankton found in 19 resevoirs and ponds that were sampled at on at least two occasions in Aguascalientes State, Mexico, at a latitude of about 21°30 North Latitude. We collected a total of 33 cladoceran taxa, 15 calanoid and cyclopoid copepods, an Ergasilus copepod, 2 anostracans, one notostracan species and an amphipod. All these taxa had previously been reported in Mexico. As in more temperate areas, there was a significant correlation between the species richness and lake size. The species-area relationship for Aguascalientes was indistinguishable from that of more northerly lakes. The two most common associations of zooplankton species were (1) those small species that occurred with fish: Daphnia parvula, Diaphanosoma birgei, Leptodiaptomus siciloides, Mastigodiaptomus albuquerquensis, and Thermocyclops inversus, and (2) the large Daphnia schodleri that occurred with the predator Notonecta, in the absence of fish. With minor variations, these two associations also occur throughout temperate North America.     

Carbinolamine formation and dehydration in a DNA repair enzyme active site

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics-molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water-independent enzyme-catalyzed reaction had a bias-corrected Jarzynski-average barrier height of approximately (6.5 kcal mol(-1) (27.2 kJ mol(-1)) for the carbinolamine formation reaction and 44.5 kcal mol(-1) (186 kJ mol(-1)) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately 15 kcal mol(-1) (62.8 kJ mol(-1)) in the forward (formation) reaction and 19 kcal mol(-1) (79.5 kJ mol(-1)) for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water-independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N-terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N-terminal amine.     

Dumontia oregonensis n. fam., n. gen., n. sp., a cladoceran representing a new family of `Water-fleas' (Crustacea,Anomopoda) from U.S.A., with notes on the classification of the Order Anomopoda

Dumontia oregonensis, a cladoceran representing a new family in the Order Anomopoda is described from rain pools in the Agate Desert, Oregon, U.S.A. The proposed family, Dumontiidae, is the newest family within Anomopoda that is not just a reshuffling of already-known species. The general appearance of this novel cladoceran is similar to that of members of the family Macrothricidae. However, a detailed examination of the trunk limbs, particularly of the second pair of limbs, showed that the new species lacks the scraper-setae typically observed in all members of the recently erected suborder Radopoda, to which macrothricids belong. Instead, limb morphology suggests a closer relation of Dumontiidae to the family Daphniidae. Dumontiidae appears to be a `missing' link between the suborder Radopoda and the `non-radopodid' anomopods. The families Daphniidae, Ilyocryptidae, Bosminidae, Moinidae and the new Dumontiidae are similar in that they lack of typical radopodid setae on the second pair of trunk limbs. Further studies on the limb morphology of non-radopodid cladocerans are required to solve the phylogenetic relationships among the members of the order Anomopoda.