Ginseng aqueous extract attenuates the production of virulence factors, stimulates twitching and adhesion, and eradicates biofilms of Pseudomonas aeruginosa

This study was carried out to examine the antimicrobial activity of the aqueous extract of Panax quinquefolius from North American ginseng (NAGE) root against Pseudomonas aeruginosa . The minimum inhibitory concentrations of reference and clinical isolates of Pseudomonas aeruginosa were measured by a standard agar-dilution method. At subinhibitory NAGE concentrations, the secretion of virulence factors, motility on agar, and adhesion to 96-well microplates were studied on the nonmucoid Pseudomonas aeruginosa O1 strain. At suprainhibitory concentrations, the activity of NAGE against mature biofilm complexes formed in the Calgary Biofilm Device and the Stovall flow cell were assessed. NAGE possessed an antibacterial activity against all the Pseudomonas aeruginosa strains at 1.25%-2.5% w/v. NAGE also significantly attenuated pyocyanin, pyoverdine, and lipase concentrations, stimulated twitching, and attenuated swarming and swimming motility. At 1.25% w/v, NAGE augmented adhesion, and at 5% w/v detached 1-day-old biofilms in microplates. The extract also eradicated 6-day-old mature biofilms (5% w/v), and fluorescence microscopy displayed a reduction of live cells and biofilm complexes compared with nontreated biofilms. These data suggest that the aqueous extract from North American ginseng possesses antimicrobial activities in vitro.     

Mutation detection with next-generation resequencing through a mediator genome

The affordability of next generation sequencing (NGS) is transforming the field of mutation analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by sequencing the entire genome of the mutant and comparing it to the wild-type (WT) genome, thus identifying acquired mutations. A major limitation for this approach is the need for an a-priori sequenced reference genome for the WT organism, as the short reads of most current NGS approaches usually prohibit de-novo genome assembly. To overcome this limitation we propose a general framework that utilizes the genome of relative organisms as mediators for comparing WT and mutant bacteria. Under this framework, both mutant and WT genomes are sequenced with NGS, and the short sequencing reads are mapped to the mediator genome. Variations between the mutant and the mediator that recur in the WT are ignored, thus pinpointing the differences between the mutant and the WT. To validate this approach we sequenced the genome of Bdellovibrio bacteriovorus 109J, an obligatory bacterial predator, and its prey-independent mutant, and compared both to the mediator species Bdellovibrio bacteriovorus HD100. Although the mutant and the mediator sequences differed in more than 28,000 nucleotide positions, our approach enabled pinpointing the single causative mutation. Experimental validation in 53 additional mutants further established the implicated gene. Our approach extends the applicability of NGS-based mutant analyses beyond the domain of available reference genomes.     

Monocytes are essential for inhibition of synovial T-cell glucocorticoid-mediated apoptosis in rheumatoid arthritis

Introduction  

Rheumatoid arthritis (RA) is characterized by synovial inflammation with local accumulation of mononuclear cells such as macrophages and lymphocytes. We previously demonstrated that intra-articular glucocorticoids decrease the synovial tissue (ST) T-cell population and therefore aimed to investigate whether this is mediated through modulation of apoptosis.     

Defense islands in bacterial and archaeal genomes and prediction of novel defense systems

The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic "sinks" that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.     

Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree

The leaf surfaces of Tamarix, a salt-secreting desert tree, harbor a diverse community of microbial epiphytes. This ecosystem presents a unique combination of ecological characteristics and imposes a set of extreme stress conditions. The composition of the microbial community along ecological gradients was studied from analyses of microbial richness and diversity in the phyllosphere of three Tamarix species in the Mediterranean and Dead Sea regions in Israel and in two locations in the United States. Over 200,000 sequences of the 16S V6 and 18S V9 hypervariable regions revealed a diverse community, with 788 bacterial and 64 eukaryotic genera but only one archaeal genus. Both geographic location and tree species were determinants of microbial community structures, with the former being more dominant. Tree leaves of all three species in the Mediterranean region were dominated by Halomonas and Halobacteria, whereas trees from the Dead Sea area were dominated by Actinomycetales and Bacillales. Our findings demonstrate that microbial phyllosphere communities on different Tamarix species are highly similar in the same locale, whereas trees of the same species that grow in different climatic regions host distinct microbial communities.     

Genetic background of patients from a university medical center in Manhattan: implications for personalized medicine

Background

The rapid progress currently being made in genomic science has created interest in potential clinical applications; however, formal translational research has been limited thus far. Studies of population genetics have demonstrated substantial variation in allele frequencies and haplotype structure at loci of medical relevance and the genetic background of patient cohorts may often be complex.

Methods and Findings

To describe the heterogeneity in an unselected clinical sample we used the Affymetrix 6.0 gene array chip to genotype self-identified European Americans (N = 326), African Americans (N = 324) and Hispanics (N = 327) from the medical practice of Mount Sinai Medical Center in Manhattan, NY. Additional data from US minority groups and Brazil were used for external comparison. Substantial variation in ancestral origin was observed for both African Americans and Hispanics; data from the latter group overlapped with both Mexican Americans and Brazilians in the external data sets. A pooled analysis of the African Americans and Hispanics from NY demonstrated a broad continuum of ancestral origin making classification by race/ethnicity uninformative. Selected loci harboring variants associated with medical traits and drug response confirmed substantial within- and between-group heterogeneity.

Conclusion

As a consequence of these complementary levels of heterogeneity group labels offered no guidance at the individual level. These findings demonstrate the complexity involved in clinical translation of the results from genome-wide association studies and suggest that in the genomic era conventional racial/ethnic labels are of little value.     

A unique reproductive strategy in the mushroom coral Fungia fungites

Coral Reefs - The vast majority of scleractinian corals are either simultaneous hermaphrodites or gonochoric. Exceptions to these are rare. Nevertheless, species belonging to the family Fungiidae...     

The Taxonomy and Phylogeny of Echinometra (Camarodonta: Echinometridae) from the Red Sea and Western Indian Ocean

The number of valid species in the genus Echinometra (Echinodermata, Echinoidea) and their associated identification keys have been debated in the scientific literature for more than 180 years. As the phylogeny and dispersal patterns of these species have been widely used as a prominent model for marine speciation, new insights into their taxonomy have the potential to deepen our understanding of marine speciation processes. In this study we examine Echinometra taxonomy, combining morphology and molecular tools. We present the taxonomy and phylogeny of Red Sea and Western Indian Ocean Echinometra. The currently available morphological keys were found to be limited in their ability to delineate all species within this genus. Nonetheless, morphological similarities between the Red Sea and Western Indian Ocean populations were high, and delimited them from the other species. These latter populations together formed a monophyletic clade, genetically distant from any of the other Echinometra species by more than 3%. Combining both traditional taxonomy and molecular evidence, we found that these populations were neither Echinometra mathaei nor E. oblonga, as previously considered. The morphological discrepancies of these populations, and their genetic divergence from the other Echinometra species, suggest that they should be considered as a new Echinometra species.