Biodecolourization of azo and triphenylmethane dyes by <Emphasis Type="Italic">Dichomitus squalens</Emphasis> and <Emphasis Type="Italic">Phlebia</Emphasis> spp

Nine white-rot fungal strains were screened for biodecolourization of brilliant green, cresol red, crystal violet, congo red and orange II. Dichomitus squalens, Phlebia fascicularia and P. floridensis decolourized all of the dyes on solid agar medium and possessed better decolourization ability than Phanerochaete chrysosporium when tested in nitrogen-limited broth medium. Journal of Industrial Microbiology & Biotechnology (2002) 28, 201–203 DOI: 10.1038/sj/jim/7000222 Received 12 July 2001/ Accepted in revised form 22 October 2001     

Bacteria in cancer therapy: a novel experimental strategy

Resistance to conventional anticancer therapies in patients with advanced solid tumors has prompted the need of alternative cancer therapies. Moreover, the success of novel cancer therapies depends on their selectivity for cancer cells with limited toxicity to normal tissues. Several decades after Coley's work a variety of natural and genetically modified non-pathogenic bacterial species are being explored as potential antitumor agents, either to provide direct tumoricidal effects or to deliver tumoricidal molecules. Live, attenuated or genetically modified non-pathogenic bacterial species are capable of multiplying selectively in tumors and inhibiting their growth. Due to their selectivity for tumor tissues, these bacteria and their spores also serve as ideal vectors for delivering therapeutic proteins to tumors. Bacterial toxins too have emerged as promising cancer treatment strategy. The most potential and promising strategy is bacteria based gene-directed enzyme prodrug therapy. Although it has shown successful results in vivo yet further investigation about the targeting mechanisms of the bacteria are required to make it a complete therapeutic approach in cancer treatment.     

Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi

Group I introns were discovered inserted at the same position in the nuclear small-subunit ribosomal DNA (nuc-ssu-rDNA) in several species of homobasidiomycetes (mushroom-forming fungi). Based on conserved intron sequences, a pair of intron-specific primers was designed for PCR amplification and sequencing of intron-containing rDNA repeats. Using the intron-specific primers together with flanking rDNA primers, a PCR assay was conducted to determine presence or absence of introns in 39 species of homobasidiomycetes. Introns were confined to the genera Panellus, Clavicorona, and Lentinellus. Phylogenetic analyses of nuc-ssu-rDNA and mitochondrial ssu-rDNA sequences suggest that Clavicorona and Lentinellus are closely related, but that Panellus is not closely related to these. The simplest explanation for the distribution of the introns is that they have been twice independently gained via horizontal transmission, once on the lineage leading to Panellus, and once on the lineage leading to Lentinellus and Clavicorona. BLAST searches using the introns from Panellus and Lentinellus as query sequences retrieved 16 other similar group I introns of nuc-ssu-rDNA and nuclear large-subunit rDNA (nuc-lsu-rDNA) from fungal and green algal hosts. Phylogenetic analyses of intron sequences suggest that the mushroom introns are monophyletic, and are nested within a clade that contains four other introns that insert at the same position as the mushroom introns, two from different groups of fungi and two from green algae. The distribution of host lineages and insertion sites among the introns suggests that horizontal and vertical transmission, homing, and transposition have been factors in intron evolution. As distinctive, heritable features of nuclear rDNAs in certain lineages, group I introns have promise as phylogenetic markers. Nevertheless, the possibility of horizontal transmission and homing also suggest that their use poses certain pitfalls.      

Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli

Six out of 12 independent replicate populations of Escherichia coli maintained in long-term glucose-limited continuous culture for up to approximately 1,750 generations evolve polymorphisms maintained by acetate crossfeeding. In all cases, the acetate-crossfeeding phenotype is associated with semiconstitutive overexpression of acetyl CoA synthetase, which allows for the enhanced uptake of low levels of exogenous acetate. Mutations in the 5' regulatory region of the acetyl CoA synthetase locus are responsible for all the acetate crossfeeding phenotypes found. These changes were either transposable-element insertions or a single T-->A nucleotide substitution at position -93 relative to the acs gene translation start site.      

Parent presence, delayed dispersal, and territory acquisition in the Seychelles warbler

The presence of parents in the natal territory may play an important,but often overlooked, role in natal dispersal and the consequentacquisition of a territory. Living with parents in a territorymay confer a fitness advantage to subordinates through, forexample, the nepotistic behavior of the parents or indirectbenefits gained by helping to raise nondescendent kin. Whena parent is replaced by a stepparent, such advantages are reducedor disappear and, as a result, subordinates may disperse. Subordinatesthat disperse after parent replacement may be constrained intheir timing of dispersal, which could have negative fitnessconsequences. In the cooperatively breeding Seychelles warbler,we show that when a parent was naturally replaced or experimentallyremoved and subsequently replaced by a stepparent from outsidethe territory, subordinates were more likely to disperse thanwhen both parents remained in the natal territory. Furthermore,subordinates dispersing from territories in which one or bothparents had been replaced were less likely to acquire a breederposition than subordinates dispersing when both parents werestill on the natal territory. Our findings suggest that thepresence of parents in the natal territory may promote delayeddispersal and facilitate the eventual acquisition of a breederposition outside the natal territory. Our results support theidea that the prolonged parental care, which long-lived speciesare able to provide, may have selected for family living.     

Virus genome dynamics under different propagation pressures: reconstruction of whole genome haplotypes of west nile viruses from NGS data

Background

Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutation-selection equilibria of population variants is greatly underestimated. The emergence of lineage 1 WNV strains has been studied extensively, but recent epidemics caused by lineage 2 WNV strains in Hungary, Austria, Greece and Italy emphasizes the increasing importance of this lineage to public health. In this study we explored the quasispecies dynamics of minority variants that contribute to cell-tropism and host determination, i.e. the ability to infect different cell types or cells from different species from Next Generation Sequencing (NGS) data of a historic lineage 2 WNV strain.

Results

Minority variants contributing to host cell membrane association persist in the viral population without contributing to the genetic change in the consensus genome. Minority variants are shown to maintain a stable mutation-selection equilibrium under positive selection, particularly in the capsid gene region.

Conclusions

This study is the first to infer positive selection and the persistence of WNV haplotype variants that contribute to viral fitness without accompanying genetic change in the consensus genotype, documented solely from NGS sequence data. The approach used in this study streamlines the experimental design seeking viral minority variants accurately from NGS data whilst minimizing the influence of associated sequence error.