Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein–double-stranded DNA and protein–single-stranded DNA complexes. The interface properties of the protein–RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein–RNA and protein–DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein–RNA complexes, backbone contacts were more dominant in the protein–DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.     

A small outbreak of listeriosis potentially linked to the consumption of imitation crab meat

A small outbreak of listeriosis involving two previously healthy adults occurred in Ontario. Food samples obtained from the refrigerator of the patients included imitation crab meat, canned black olives, macaroni and vegetable salad, spaghetti sauce with meatballs, mayonnaise and water. All of the samples except the water contained Listeria monocytogenes. The three most heavily contaminated samples were the imitation crab meat, the olives and the salad which contained 2.1 x 109, 1.1 x 107 and 1.3 x 106 cfu g-1, respectively. L. monocytogenes serotype 1/2b was isolated from the patients, as well as from the opened and unopened imitation crab meat. Molecular typing of the isolates by both randomly amplified polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) typing demonstrated the imitation crab meat and clinical strains to be indistinguishable. Challenge studies performed with a pool of L. monocytogenes strains showed that imitation crab meat, but not olives, supported growth of the organism. In this study we have shown for the first time the potential involvement of imitation crab meat in a small outbreak of listeriosis. In terms of disease prevention, temperature control is critical to prevent or reduce the growth of this foodborne pathogen. In addition, with refrigerated products having a long (> 30 d) shelf life, additional safety factors must be used to prevent the growth of foodborne pathogens such as L. monocytogenes.     

Shallow genetic and morphological divergence among seaperches in the South Pacific (family Scorpaenidae; genus Helicolenus)

The phylogenetic relationships among populations of seaperch, Helicolenus spp., in the south-west Pacific were examined with mtDNA markers. Parts of the cytochrome b gene [459 base pair (bp)] and the control region (448 bp) were sequenced in 58 specimens from the south-west Pacific and four specimens of Helicolenus lengerichi from Chile. Only one clade was recognized in New Zealand coastal waters, despite a wide range of colour morphs. This clade also occurred in the mid Tasman Sea on the Norfolk Ridge and around Tasmania and Victoria. A second sympatric clade was identified around Tasmania and Victoria and to the west of New Zealand. A third allopatric clade was identified to the north of New Zealand and in deep water on the Chatham Rise and a fourth clade on the Foundation Seamounts and the Louisville Ridge. Helicolenus lengerichi from Chile formed a fifth clade. Assuming a molecular clock, the clades were estimated to have diverged c. 0·7–2·6 million years ago. Only two clades, around Tasmania and Victoria, were separated using morphology, colour (in live) and dorsal-fin soft ray counts and were confirmed as Helicolenus percoides and Helicolenus barathri . Two characters, orbit diameter and colour variation, previously used to identify two species in New Zealand waters were unreliable characters for species discrimination. Principle component analyses of 11 morphological measures from 67 individuals did not delineate the clades. A canonical discriminant analysis was able to separate four of the five clades, but mean discriminate probabilities were low (77·6%), except for the five Chilean specimens of H. lengerichi (100%).     

Sonic Hedgehog Controls the Phenotypic Fate and Therapeutic Efficacy of Grafted Neural Precursor Cells in a Model of Nigrostriatal Neurodegeneration

The expression of soluble growth and survival promoting factors by neural precursor cells (NPCs) is suggested to be a prominent mechanism underlying the protective and regenerative effects of these cells after transplantation. Nevertheless, how and to what extent specific NPC-expressed factors contribute to therapeutic effects is not well understood. Using RNA silencing, the current study investigated the roles of two donor NPC molecules, namely glial cell-line derived neurotrophic factor (GDNF) and sonic hedgehog (SHH), in the protection of substantia nigra dopamine neurons in rats treated with 6-hydroxydopamine (6-OHDA). Analyses indicate that as opposed to the knock-down of GDNF, SHH inhibition caused a profound decline in nigrostriatal neuroprotection. Further, SHH silencing also curbed endogenous neurogenesis and the migration of host brdU⁺/dcx⁺ neural precursors into the striatum, which was present in the animals receiving control or GDNF silenced NPCs. A change in graft phenotype, mainly reflected by a reduced proportion of undifferentiated nestin⁺ cells, as well as a significantly greater host microglial activity, suggested an important role for these processes in the attenuation of neuroprotection and neurogenesis upon SHH silencing. Overall these studies reveal core mechanisms fundamental to grafted NPC-based therapeutic effects, and delineate the particular contributions of two graft-expressed molecules, SHH and GDNF, in mediating midbrain dopamine neuron protection, and host plasticity after NPC transplantation.     

Two explanations for the compliant running paradox: reduced work of bouncing viscera and increased stability in uneven terrain

Economy is a central principle for understanding animal locomotion. Yet, compared with theoretical predictions concerning economy, animals run with compliant legs that are energetically costly. Here, we address this apparent paradox, highlighting two factors that predict benefits for compliant gaits: (i) minimizing cost of work associated with bouncing viscera; and (ii) leg control for robust stability in uneven terrain. We show that consideration of the effects of bouncing viscera predicts an energetic optimum for relatively compliant legs. To compare stability in uneven terrain, we introduce the normalized maximum drop (NMD), a measure based on simple kinematics, which predicts that compliant legs allow negotiation of relatively larger terrain perturbations without failure. Our model also suggests an inherent trade-off in control of leg retraction velocity (ω) for stability: low ω allows higher NMD, reducing fall risk, whereas high ω minimizes peak forces with terrain drops, reducing injury risk. Optimization for one of these factors explicitly limits the other; however, compliant legs relax this trade-off, allowing greater stability by both measures. Our models suggest compromises in leg control for economy and stability that might explain why animals run with compliant legs.     

Antibiotic susceptibility of coagulase-negative staphylococci isolated from very low birth weight babies: comprehensive comparisons of bacteria at different stages of biofilm formation

Background

Coagulase-negative staphylococci are major causes of bloodstream infections in very low birth weight babies cared for in Neonatal Intensive Care Units. The virulence of these bacteria is mainly due to their ability to form biofilms on indwelling medical devices. Biofilm-related infections often fail to respond to antibiotic chemotherapy guided by conventional antibiotic susceptibility tests.

Methods

Coagulase-negative staphylococcal blood culture isolates were grown in different phases relevant to biofilm formation: planktonic cells at mid-log phase, planktonic cells at stationary phase, adherent monolayers and mature biofilms and their susceptibilities to conventional antibiotics were assessed. The effects of oxacillin, gentamicin, and vancomycin on preformed biofilms, at the highest achievable serum concentrations were examined. Epifluorescence microscopy and confocal laser scanning microscopy in combination with bacterial viability staining and polysaccharide staining were used to confirm the stimulatory effects of antibiotics on biofilms.

Results

Most coagulase-negative staphylococcal clinical isolates were resistant to penicillin G (100%), gentamicin (83.3%) and oxacillin (91.7%) and susceptible to vancomycin (100%), ciprofloxacin (100%), and rifampicin (79.2%). Bacteria grown as adherent monolayers showed similar susceptibilities to their planktonic counterparts at mid-log phase. Isolates in a biofilm growth mode were more resistant to antibiotics than both planktonic cultures at mid-log phase and adherent monolayers; however they were equally resistant or less resistant than planktonic cells at stationary phase. Moreover, for some cell-wall active antibiotics, concentrations higher than conventional MICs were required to prevent the establishment of planktonic cultures from biofilms. Finally, the biofilm-growth of two S. capitis isolates could be enhanced by oxacillin at the highest achievable serum concentration.

Conclusion

We conclude that the resistance of coagulase-negative staphylococci to multiple antibiotics initially remain similar when the bacteria shift from a planktonic growth mode into an early attached mode, then increase significantly as the adherent mode further develops. Furthermore, preformed biofilms of some CoNS are enhanced by oxacillin in a dose-dependent manner.     

Leg muscles that mediate stability: mechanics and control of two distal extensor muscles during obstacle negotiation in the guinea fowl

Here, we used an obstacle treadmill experiment to investigate the neuromuscular control of locomotion in uneven terrain. We measured in vivo function of two distal muscles of the guinea fowl, lateral gastrocnemius (LG) and digital flexor-IV (DF), during level running, and two uneven terrains, with 5 and 7 cm obstacles. Uneven terrain required one step onto an obstacle every four to five strides. We compared both perturbed and unperturbed strides in uneven terrain to level terrain. When the bird stepped onto an obstacle, the leg became crouched, both muscles acted at longer lengths and produced greater work, and body height increased. Muscle activation increased on obstacle strides in the LG, but not the DF, suggesting a greater reflex contribution to LG. In unperturbed strides in uneven terrain, swing pre-activation of DF increased by 5 per cent compared with level terrain, suggesting feed-forward tuning of leg impedance. Across conditions, the neuromechanical factors in work output differed between the two muscles, probably due to differences in muscle-tendon architecture. LG work depended primarily on fascicle length, whereas DF work depended on both length and velocity during loading. These distal muscles appear to play a critical role in stability by rapidly sensing and responding to altered leg-ground interaction.