Sampling properties of DNA sequence data in phylogenetic analysis

We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.      

Some observations on the effect of Daflon (micronized purified flavonoid fraction of Rutaceae aurantiae) in bancroftian filarial lymphoedema

BACKGROUND: Morbidity management is a core component of the global programme for the elimination of lymphatic filariasis. In a double-blind clinical trial, the tolerability and efficacy of Daflon (500 mg) + DEC (25 mg) or DEC (25 mg) alone, twice daily for 90 days, was studied in 26 patients with bancroftian filarial lymphoedema. RESULTS: None of the patients in either drug group reported any adverse reaction throughout the treatment period (90 days). Haematological and biochemical parameters were within normal limits and there was no significant difference between the pre-treatment (day 0) and post-treatment (day 90) values. The group receiving Daflon showed significant reduction in oedema volume from day 90 (140.6 PlusMinus; 18.8 ml) to day 360 (71.8 PlusMinus; 20.7 ml) compared to the pre-treatment (day 0, 198.4 PlusMinus; 16.5 ml) value. This accounted for a 63.8% reduction in oedema volume by day 360 (considering the pre-treatment (day 0) as 100%). In the DEC group, the changes in oedema volume (between day 1 and day 360) were not significant when compared to the pre-treatment (day 0) value. The percentage reduction at day 360 was only 9%, which was not significant (P > 0.05). CONCLUSION: This study has shown that Daflon (500 mg, twice a day for 90 days) is both safe and efficacious in reducing oedema volume in bancroftian filarial lymphoedema. Further clinical trials are essential for strengthening the evidence base on the role of this drug in the morbidity management of lymphatic filariasis.     

Proteome analyses of cellular proteins in methicillin-resistant Staphylococcus aureus treated with rhodomyrtone, a novel antibiotic candidate

The ethanolic extract from Rhodomyrtus tomentosa leaf exhibited good antibacterial activities against both methicillin-resistant Staphylococcus aureus (MRSA) and S. aureus ATCC 29213. Its minimal inhibitory concentration (MIC) values ranged from 31.25-62.5 μg/ml, and the minimal bactericidal concentration (MBC) was 250 μg/ml. Rhodomyrtone, an acylphloroglucinol derivative, was 62.5-125 times more potent at inhibiting the bacteria than the ethanolic extract, the MIC and MBC values were 0.5 μg/ml and 2 μg/ml, respectively. To provide insights into antibacterial mechanisms involved, the effects of rhodomyrtone on cellular protein expression of MRSA have been investigated using proteomic approaches. Proteome analyses revealed that rhodomyrtone at subinhibitory concentration (0.174 μg/ml) affected the expression of several major functional classes of whole cell proteins in MRSA. The identified proteins involve in cell wall biosynthesis and cell division, protein degradation, stress response and oxidative stress, cell surface antigen and virulence factor, and various metabolic pathways such as amino acid, carbohydrate, energy, lipid, and nucleotide metabolism. Transmission electron micrographs confirmed the effects of rhodomyrtone on morphological and ultrastructural alterations in the treated bacterial cells. Biological processes in cell wall biosynthesis and cell division were interrupted. Prominent changes including alterations in cell wall, abnormal septum formation, cellular disintegration, and cell lysis were observed. Unusual size and shape of staphylococcal cells were obviously noted in the treated MRSA. These pioneer findings on proteomic profiling and phenotypic features of rhodomyrtone-treated MRSA may resolve its antimicrobial mechanisms which could lead to the development of a new effective regimen for the treatment of MRSA infections.     

Antagonistic activity against pathogenic bacteria by human vaginal lactobacilli

This study attempted to isolate lactobacilli strains from healthy vaginal ecosystem to search for a new effective antibacterial probiotic strain. The strains were identified and characterized for their probiotic properties including bile salt and acid tolerance, growth at acidic pH, their ability to utilize protein, starch, and lipid, the production of hydrogen peroxide and bacteriocin as well as their antibiotic resistance patterns. The antibacterial activity of the culture supernatant of these strains were tested against a wide range of Gram-positive and Gram-negative pathogenic bacteria including Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae. Salmonella typhi, and Salmonella typhimurium. None of the strains inhibited the growth of Gram-negative bacteria. Contrastly, the culture supernatant of strain L 22, identified as Lactobacillus reuteri, significantly inhibited all of the clinical isolates of methicillin-resistant S. aureus (MRSA). The antibacterial effect of the selected strain L 22 was further investigated. In the presence of L 22, the bacterial growth was assessed in vitro by viable bacterial counting. The numbers of viable cells were significantly lower in L 22-containing broth than those in the control by 6h. This finding clearly demonstrates that strain L 22 can produce an anti-MRSA effect. The antibacterial ability of the strain L 22 was fundamentally attributed to their bacteriocin production which can cause both cell inhibition and cell death.     

Anti Propionibacterium acnes activity of rhodomyrtone, an effective compound from Rhodomyrtus tomentosa (Aiton) Hassk. leaves

Propionibacterium acnes have been recognized as one of the main causative agents in pathogenesis of acne. Twenty one isolates of P. acnes isolated from acne lesions were screened for lipase and protease activity which are reported to be associated in acne and inflammation. Interestingly, all P. acnes isolates demonstrated lipase activity. Similarly, 90% of test P. acnes produced protease enzyme. Antibacterial activity of the ethanol extract of Rhodomyrtus tomentosa (Aiton) Hassk. leaves and rhodomyrtone, its principle compound were tested against P. acnes using broth macrodilution method. The MIC(90) values of the ethanol extract and rhodomyrtone were 32 and 0.5 μg/mL, respectively. The numbers of the bacterial cells were reduced at least 99% after treatment with the ethanol extract and rhodomyrtone within 72 and 24 h, respectively. Cytotoxicity test of the extract and rhodomyrtone was performed on human normal fibroblast. The IC(50) values of the ethanol extract and rhodomyrtone were 476 and more than 200 μg/mL, approximately 15 and 400 folds higher than the MIC(90) values indicating that both substances were very low cytotoxic which could be applied as topical therapeutic anti-acne agents.     

Boesenbergia pandurata (Roxb.) Schltr., Eleutherine americana Merr. and Rhodomyrtus tomentosa (Aiton) Hassk. as antibiofilm producing and antiquorum sensing in Streptococcus pyogenes

Biofilm formation has been demonstrated as a potentially important mechanism contributing to antibiotic treatment failure on Streptococcus pyogenes. It could play a significant role in recurrent and chronic infections. Boesenbergia pandurata (Roxb.) Schltr., Eleutherine americana Merr. and Rhodomyrtus tomentosa (Aiton) Hassk. have been previously reported from our laboratory as effective agents against S. pyogenes. Therefore, in the present study, we observed the effect of these plants on biofilm formation. The bacterial biofilms were quantified by safranin staining and absorbance at 492 nm. The results clearly demonstrated that all subinhibitory concentrations [1/32-1/2 minimal inhibitory concentration (MIC)] of E. americana (7.81-125 microg mL(-1)) and R. tomentosa (0.24-7.81 microg mL(-1)) extracts significantly prevented biofilm formation while 1/2MIC (7.81 microg mL(-1)) of B. pandurata extract produced this effect. The issue of antiquorum sensing of this pathogenic bacterium has been further explored. A correlation between antiquorum-sensing and antibiofilm-producing activities was demonstrated. Strong inhibition on quorum sensing was displayed with the extract of R. tomentosa. Eleutherine americana extract showed partial inhibition, while B. pandurata did not show this activity. By contrast, an assay of microbial adhesion to hydrocarbon revealed no changes in the cell-surface hydrophobicity of the treated organisms. Active organisms with the ability to inhibit quorum sensing and biofilm formation are worth studying as they may provide complimentary medicine for biofilm-associated infections.     

Effect of subinhibitory concentrations of antimicrobial agents (quinolones and macrolide) on the production of verotoxin by enterohemorrhagic Escherichia coli O157:H7.

In Japan, antimicrobial agent therapy for patients with diarrhea due to enterovirulent organisms including enterohemorrhagic Escherichia coli (EHEC) is common, and norfloxacin (NFLX), fosfomycin, and kanamycin are recommended for EHEC treatment by the Japanese Ministry of Health and Welfare. The aim of this study was to analyze the effects of antimicrobial agents which have been used or recommended for the treatment of EHEC on the production of verotoxin (VT) in vitro. Subinhibitory concentrations of quinolones, NFLX, sparofloxacin (SPFX), and grepafloxacin (GPFX) markedly stimulated the productions of VT1 and VT2. The macrolide azithromycin (AZM), erythromycin (EM), and clarithromycin (CAM) did not stimulate the production of VT at a wide range of concentrations. These in vitro results indicate that when quinolones are prescribed for a patient infected with EHEC, the concentration of antimicrobial agents used in vivo and the susceptibility of the EHEC strains against quinolones should be taken into consideration.     

Mesozooplankton of the Kosi Bay lakes,South Africa

The Kosi coastal lake system, a chain of four interconnected basins, is located in the subtropical north-eastern corner of South Africa. Little information is available on zooplankton of the system and the main aim of this study is to report on zooplankton samples collected during 2002 and 2003. The set of samples consists of seasonal, subsurface mesozooplankton samples that were collected during nighttime in each of the lakes. A well-developed salinity gradient was evident along the interconnected lakes in the subsurface water during all seasons, ranging from freshwater in the upper lake Amanzamnyama to a maximum of 22 recorded in Lake Makhawulani. The zooplankton community structures of the lakes reflected the salinity gradient of the system, with some coastal marine taxa recorded in the lakes closer to the mouth and only freshwater taxa recorded in Lake Amanzamnyama. Mesozooplankton diversity and abundance were relatively low compared to other estuarine systems along the eastern coast of South Africa. The dominant taxa were calanoid copepods Acartiella natalensis and Pseudodiaptomus stuhlmanni and the mysid Mesopodopsis africana in the lower lakes, whereas cyclopoids Mesocyclops sp. and Thermocyclops sp. dominated the freshwater lake Amanzamnyama.