The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining

The robustness (sensitivity to violation of assumptions) of the maximum- likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes- Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of the methods were violated to varying degrees on three model four-taxon trees. The performance of the methods was evaluated with respect to ability to correctly estimate the unrooted four-taxon tree. Maximum likelihood outperformed neighbor joining in 29 of the 36 cases in which the assumptions of both methods were satisfied. In 133 of 180 of the simulations in which the assumptions of the maximum-likelihood and neighbor-joining methods were violated, maximum likelihood outperformed neighbor joining. These results are consistent with a general superiority of maximum likelihood over neighbor joining under comparable conditions. They extend and clarify an earlier study that found an advantage for neighbor joining over maximum likelihood for gamma-distributed mutation rates.      

How much ozone bactericidal activity is compromised by plasma components?

Aims:  Evaluation of bactericidal effect of different concentrations of ozone when used (a) as a gas, or (b) dissolved in saline. The addition of hydrogen peroxide or 4-hydroxynonenal dissolved in saline was also tested, as well as the effect of human plasma.
Methods and Results:  Staphylococcus aureus , methicillin-resistant Staph. aureus (MRSA), and Pseudomonas aeruginosa , suspended in their culture media were tested. While all bacteria suspended in protein-free saline were killed at high ozone concentrations, they survived when as little as 5% human plasma was present. Hydrogen peroxide was 100-fold less active than ozone and needed to remain in contact with bacteria for at least 60 min. 4-hydroxynonenal (2 μmol l⁻¹) was inhibitory for proliferation of both Staph. aureus and MRSA, but not for Ps. aeruginosa .
Conclusions:  Ozone and the cascade of its derivative products are potent bactericidal agents, but even small amounts of human plasma, hence of hydro- and liposoluble antioxidants, in bacterial suspensions inhibit oxidation and protect bacteria.
Significance and Impact of the Study:  Any substantial in vivo cytocidal effect of ozone and its derivatives can be excluded. On the other hand, topical and continuous action of various ozone preparations remains valuable in a variety of skin and mucosal infections.     

Electrotransformation studies in Clostridium cellulolyticum

Electropermeabilization of Clostridium cellulolyticum was optimized using ATP leakage assays. Electrotransformation was then performed under optimized conditions (6 to 7.5 kV cm⁻¹ field strength applied during 5 ms to a mixture containing methylated plasmids and late exponential phase cell suspensions (10 molecules:1 cell) in a sucrose-containing buffer). Transformants were only obtained when 7 or 7.5 kV cm⁻¹ pulses were applied. Transformation efficiencies evaluated from the growth curves of transformed cells were between 10⁵ and 10⁷ transformants per microgram of plasmid DNA for five different replicon-based plasmids. Restriction nuclease digestion patterns of pJIR418 purified from transformed Clostridia and Escherichia coli were indistinguishable, indicating that heterologous DNA was structurally stable in the Clostridium strain. Copy numbers of 130, 70 and 10 were estimated from purification yield for pCTC1, pKNT19 and pJIR418, respectively. Journal of Industrial Microbiology & Biotechnology (2001) 27, 271–274. Received 12 September 2000/ Accepted in revised form 25 November 2000     

Effects of pancreatic polypeptide on pancreas-projecting rat dorsal motor nucleus of the vagus neurons

We investigated the pre- and postsynaptic effects of pancreatic polypeptide (PP) on identified pancreas-projecting neurons of the rat dorsal motor nucleus of the vagus in thin brain stem slices. Perfusion with PP induced a TTX- and apamin-sensitive, concentration-dependent outward (22% of neurons) or inward current (21% of neurons) that was accompanied by a decrease in input resistance; PP was also found to affect the amplitude of the action potential afterhyperpolarization. The remaining 57% of neurons were unaffected. PP induced a concentration-dependent inhibition in amplitude of excitatory (n = 22 of 30 neurons) and inhibitory (n = 13 of 17 neurons) postsynaptic currents evoked by electrical stimulation of the adjacent nucleus of the solitary tract, with an estimated EC(50) of 30 nM for both. The inhibition was accompanied by an alteration in the paired pulse ratio, suggesting a presynaptic site of action. PP also decreased the frequency, but not amplitude, of spontaneous excitatory (n = 6 of 11 neurons) and inhibitory currents (n = 7 of 9 neurons). In five neurons, chemical stimulation of the area postrema (AP) induced a TTX-sensitive inward (n = 3) or biphasic (outward and inward) current (n = 2). Superfusion with PP reversibly reduced the amplitude of these chemically stimulated currents. Regardless of the PP-induced effect, the vast majority of responsive neurons had a multipolar somata morphology with dendrites projecting to areas other than the fourth ventricle or the central canal. These results suggest that pancreas-projecting rat dorsal motor nucleus of the vagus neurons are heterogeneous with respect to their response to PP, which may underlie functional differences in the vagal modulation of pancreatic functions.     

<Emphasis Type="Italic">Candida albicans</Emphasis>genome sequence: a platform for genomics in the absence of genetics

Publication of the complete diploid genome sequence of the yeast Candida albicans will accelerate research into the pathogenesis of Candida infections. Comparative genomic analysis highlights genes that may contribute to C. albicans survival and its fitness as a human commensal and pathogen.     

Microbial signaling and systems biology

A report of the symposium on Signaling and Systems Biology held during the Society for General Microbiology Spring Meeting, 29-30 March 2010, Edinburgh, UK.     

Consequences of concurrent Ascaridia galli and Escherichia coli infections in chickens

   

The principal aim of this study was to evaluate dissociative anaesthesia for castration of colts during field conditions. Three dissociative anaesthetic protocols were evaluated during castration of colts in an animal hospital. The protocol considered to be the most suitable was thereafter evaluated during castration of colts under field conditions. Respiratory and haemodynamic parameters and the response to surgery were determined during anaesthesia. All horses breathed air spontaneously during anaesthesia. Under hospital conditions 26 colts were randomised to receive one of three anaesthetic protocols: Romifidine and tiletamine-zolazepam (RZ); acepromazine, romifidine and tiletamine-zolazepam (ARZ); or acepromazine, romifidine, butorphanol and tiletamine-zolazepam (ARBZ). The surgeon was blinded to the anaesthetic protocol used and decided whether supplemental anaesthesia was needed to complete surgery. Under field conditions 31 colts were castrated during anaesthesia with the ARBZ protocol. All inductions, anaesthesia and recoveries were calm and without excitation under both hospital and field conditions. Surgery was performed within 5–20 minutes after the horses had assumed lateral recumbency during both hospital and field castrations. Under hospital conditions some horses needed supplemental anaesthesia with all three anaesthetic protocols to complete surgery. Interestingly, none of the horses castrated with protocol ARBZ under field conditions needed additional anaesthesia. Cardiorespiratory changes were within acceptable limits in these clinically healthy colts.     

A comparison of the illness beliefs of people with angina and their peers: a questionnaire study

Background  

What people believe about their illness may affect how they cope with it. It has been suggested that such beliefs stem from those commonly held within society . This study compared the beliefs held by people with angina, regarding causation and coping in angina, with the beliefs of their friends who do not suffer from angina.