Thioredoxin reductase is essential for viability in the fungal pathogen Cryptococcus neoformans

Thioredoxin reductase (TRR1) is an important component of the thioredoxin oxidative stress resistance pathway. Here we show that it is induced during oxidative and nitrosative stress and is preferentially localized to the mitochondria in Cryptococcus neoformans. The C. neoformans TRR1 gene encodes the low-molecular-weight isoform of the thioredoxin reductase enzyme, which shares little homology with that of its mammalian host. By replacing the endogenous TRR1 promoter with an inducible copper transporter promoter, we showed that Trr1 appears to be essential for viability of this pathogenic fungus, making it a potential antifungal target.     

Resident plant diversity and introduced earthworms have contrasting effects on the success of invasive plants

Theoretical predictions and empirical studies suggest that resident species diversity is an important driver of community invasibility. Through trait-based processes, plants in communities with high resident species diversity occupy a wider range of ecological niches and are more productive than low diversity communities, potentially reducing the opportunities for invasion through niche preemption. In terrestrial plant communities, biotic ecosystem engineers such as earthworms can also affect invasibility by reducing leaf litter stocks and influencing soil conditions. In a greenhouse experiment, we simultaneously manipulated resident species diversity and earthworm presence to investigate independent and interactive effects of these two variables on the success of several invasive plants. Higher diversity of resident species was associated with lower biomass of invasives, with the effect mediated through resident species biomass. The presence of earthworms had a strong positive effect on the biomass of invasive species across all levels of resident species diversity and a weaker indirect negative effect via decreased soil moisture. Earthworms also weakened the positive correlation between resident species diversity and productivity. We did not observe any interactive effects of resident species biomass and earthworms on invasive species success. Partitioning the net biodiversity effect indicated that selection effects increased with resident species diversity whereas complementarity effects did not. Results suggest that managing for diverse forest communities may decrease the susceptibility of these communities to invasions. However, the presence of introduced earthworms in previously earthworm-free sites may undermine these efforts. Furthermore, future studies of plant community invasibility should account for the effects of introduced earthworms.     

Chitosan, the deacetylated form of chitin, is necessary for cell wall integrity in Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic fungal pathogen that causes cryptococcal meningoencephalitis, particularly in immunocompromised patients. The fungal cell wall is an excellent target for antifungal therapies as it is an essential organelle that provides cell structure and integrity, it is needed for the localization or attachment of known virulence factors, including the polysaccharide capsule, melanin, and phospholipase, and it is critical for host-pathogen interactions. In C. neoformans, chitosan produced by the enzymatic removal of acetyl groups from nascent chitin polymers has been implicated as an important component of the vegetative cell wall. In this study, we identify four putative chitin/polysaccharide deacetylases in C. neoformans. We have demonstrated that three of these deacetylases, Cda1, Cda2, and Cda3, can account for all of the chitosan produced during vegetative growth in culture, but the function for one, Fpd1, remains undetermined. The data suggest a model for chitosan production in vegetatively growing C. neoformans where the three chitin deacetylases convert chitin generated by the chitin synthase Chs3 into chitosan. Utilizing a collection of chitin/polysaccharide deacetylase deletion strains, we determined that during vegetative growth, chitosan helps to maintain cell integrity and aids in bud separation. Additionally, chitosan is necessary for maintaining normal capsule width and the lack of chitosan results in a "leaky melanin" phenotype. Our analysis indicates that chitin deacetylases and the chitosan made by them may prove to be excellent antifungal targets.     

Streamlining genomes: toward the generation of simplified and stabilized microbial systems

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Highlights? Top-down and bottom-up approaches to genome streamlining. ? Computational support for constructing and refactoring streamlined genomes. ? From genome engineering to metabolic reprogramming. ? Perspectives in applied genome engineering.     

An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters

Background  

Many studies have provided algorithms or methods to assess a statistical significance in quantitative proteomics when multiple replicates for a protein sample and a LC/MS analysis are available. But, confidence is still lacking in using datasets for a biological interpretation without protein sample replicates. Although a fold-change is a conventional threshold that can be used when there are no sample replicates, it does not provide an assessment of statistical significance such as a false discovery rate (FDR) which is an important indicator of the reliability to identify differentially expressed proteins. In this work, we investigate whether differentially expressed proteins can be detected with a statistical significance from a pair of unlabeled protein samples without replicates and with only duplicate LC/MS injections per sample. A FDR is used to gauge the statistical significance of the differentially expressed proteins.     

Mutagenic activity of propylene oxide in bacterial and mammalian systems.

Propylene oxide is used extensively in the chemical and food manufacturing industries, but relatively little is known of its ability to interact with genetic material. Studies were undertaken to investigate its ability to induce gene mutations and primary DNA damage in bacteria and chromosomal damage in mammalian cells. The induction of base-substitution mutations was demonstrated in spot tests with strains of Salmonella typhimurium and Escherichia coli at 700 micrograms/plate of propylene oxide; inclusion of a preparation of rat-liver microsomes and cofactors (S9 mix) was without significant effect on this response. A linear dose--response relationship was recorded in plate tests with S. typhimurium strains TA100 and TA1535 over the range 100--750 micrograms/plate. After addition to dividing lymphocytes in cultures established from human peripheral blood, propylene oxide caused dose-related chromosomal damage, detected at 1.85 and 9.25 micrograms/ml. Oral administration of propylene oxide at 2 x 100, 2 x 250 or 2 x 500 mg/kg to male mice produced no detectable increases in the incidence of micronucleated, polychromatic erythrocytes in bone marrow. A male mouse dominant lethal test employing oral doses of 50 or 250 mg/kg/day for 14 days gave no evidence of mutagenic action on sperm. Intraperitoneal injections of propylene oxide at 2 x 300 mg/kg induced increased numbers of micronucleated erythrocytes in mice, but lower doses given by this route had no such effect. Possible reasons for the contrasting findings in vitro and in vivo are discussed.     

Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.     

Potential CRF1R PET imaging agents: 1-Fluoroalkylsubstituted 5-halo-3-(arylamino)pyrazin-2(1H)-ones

A series of pyrazinones were prepared and evaluated as potential CRF₁R PET imaging agents. Optimization of their CRF₁R binding potencies and octanol–phosphate buffer phase distribution coefficients are discussed herein.