Antimicrobial activities of marine fungi from Malaysia

Copyright 2011 Elsevier B.V., All rights reserved.Peer reviewedPublisher PD

CPT Violation Implies Violation of Lorentz Invariance

An interacting theory that violates CPT invariance necessarily violates Lorentz invariance. On the other hand, CPT invariance is not sufficient for out-of-cone Lorentz invariance. Theories that violate CPT by having different particle and antiparticle masses must be nonlocal.Comment: Minor changes in the published versio

Community Aliveness: Discovering Interaction Decay Patterns in Online Social Communities

Online Social Communities (OSCs) provide a medium for connecting people, sharing news, eliciting information, and finding jobs, among others. The dynamics of the interaction among the members of OSCs is not always growth dynamics. Instead, a $\textit{decay}$ or $\textit{inactivity}$ dynamics often happens, which makes an OSC obsolete. Understanding the behavior and the characteristics of the members of an inactive community help to sustain the growth dynamics of these communities and, possibly, prevents them from being out of service. In this work, we provide two prediction models for predicting the interaction decay of community members, namely: a Simple Threshold Model (STM) and a supervised machine learning classification framework. We conducted evaluation experiments for our prediction models supported by a $\textit{ground truth}$ of decayed communities extracted from the StackExchange platform. The results of the experiments revealed that it is possible, with satisfactory prediction performance in terms of the F1-score and the accuracy, to predict the decay of the activity of the members of these communities using network-based attributes and network-exogenous attributes of the members. The upper bound of the prediction performance of the methods we used is $0.91$ and $0.83$ for the F1-score and the accuracy, respectively. These results indicate that network-based attributes are correlated with the activity of the members and that we can find decay patterns in terms of these attributes. The results also showed that the structure of the decayed communities can be used to support the alive communities by discovering inactive members.Comment: pre-print for the 4th European Network Intelligence Conference - 11-12 September 2017 Duisburg, German

Redox Potential: Monitoring and Role in Development of Aroma Compounds, Rheological Properties and Survival of Oxygen Sensitive Strains During the Manufacture of Fermented Dairy Products

International audienc

Hawks and Doves on Small-World Networks

We explore the Hawk-Dove game on networks with topologies ranging from regular lattices to random graphs with small-world networks in between. This is done by means of computer simulations using several update rules for the population evolutionary dynamics. We find the overall result that cooperation is sometimes inhibited and sometimes enhanced in those network structures, with respect to the mixing population case. The differences are due to different update rules and depend on the gain-to-cost ratio. We analyse and qualitatively explain this behavior by using local topological arguments.Comment: 12 pages, 8 figure

Molecular epidemiology of Powassan virus in North America

Powassan virus (POW) is a tick-borne flavivirus distributed in Canada, the northern USA and the Primorsky region of Russia. POW is the only tick-borne flavivirus endemic to the western hemisphere, where it is transmitted mainly between Ixodes cookei and groundhogs (Marmota monax). Deer tick virus (DTV), a genotype of POW that has been frequently isolated from deer ticks (Ixodes scapularis), appears to be maintained in an enzootic cycle between these ticks and white-footed mice (Peromyscus leucopus). DTV has been isolated from ticks in several regions of North America, including the upper Midwest and the eastern seaboard. The incidence of human disease due to POW is apparently increasing. Previous analysis of tick-borne flaviviruses endemic to North America have been limited to relatively short genome fragments. We therefore assessed the evolutionary dynamics of POW using newly generated complete and partial genome sequences. Maximum-likelihood and Bayesian phylogenetic inferences showed two well-supported, reciprocally monophyletic lineages corresponding to POW and DTV. Bayesian skyline plots based on year-of-sampling data indicated no significant population size change for either virus lineage. Statistical model-based selection analyses showed evidence of purifying selection in both lineages. Positive selection was detected in NS-5 sequences for both lineages and envelope sequences for POW. Our findings confirm that POW and DTV sequences are relatively stable over time, which suggests strong evolutionary constraint, and support field observations that suggest that tick-borne flavivirus populations are extremely stable in enzootic foci

Strong electric fields induced on a sharp stellar boundary

Due to a first order phase transition, a compact star may have a discontinuous distribution of baryon as well as electric charge densities, as e.g. at the surface of a strange quark star. The induced separation of positive and negative charges may lead to generation of supercritical electric fields in the vicinity of such a discontinuity. We study this effect within a relativistic Thomas-Fermi approximation and demonstrate that the strength of the electric field depends strongly on the degree of sharpness of the surface. The influence of strong electric fields on the stability of compact stars is discussed. It is demonstrated that stable configurations appear only when the counter-pressure of degenerate fermions is taken into consideration.Comment: 13 pages, 2 figure

New insights into the regulatory pathways associated with the activation of the stringent response in bacterial resistance to the PBP2-targeted antibiotics, mecillinam and OP0595/RG6080

Objectives: The diazabicyclooctane β-lactamase inhibitor OP0595 (RG6080) also acts as an antibiotic, targeting PBP2 in Enterobacteriaceae, but this activity is vulnerable to mutational resistance. We used WGS to investigate the basis of this resistance. Methods: Twenty OP0595-selected mutants, comprising four derived from each of five different Escherichia coli strains, were sequenced on Illumina HiSeq. Reads from each mutant were mapped to the assembled genome of the corresponding parent. A variant-calling file generated with Samtools was parsed to determine genetic alterations. Results: Besides OP0595, the mutants consistently showed decreased susceptibility to mecillinam, which likewise targets PBP2, and grew as stable round forms in the presence of subinhibitory concentrations of OP0595. Among the 20 mutants, 18 had alterations in genes encoding tRNA synthase and modification functions liable to induce expression of the RpoS sigma factor through activation of the stringent response or had mutations suppressing inactivators of RpoS or the stringent response signal-degrading enzyme, SpoT. TolB was inactivated in one mutant: this activates RcsBC regulation and was previously associated with mecillinam resistance. The mechanism of resistance remained unidentified in one mutant. Both the RpoS and RcsBC systems regulate genes of cell division, including ftsAQZ that can compensate for loss or inhibition of PBP2, allowing survival of the challenged bacteria as stable round forms, as seen. Conclusions: WGS identified the global stringent response signal, entailing induction of RpoS, as the main mediator of mutational resistance to OP0595 in E. coli

Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges

Marine sponge–associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of < 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values <20 μg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes

Metabolomics and dereplication strategies in the discovery of natural product derived drugs

Metabolomics is the technology designed to provide general qualitative and quantitative profile of metabolites in organisms exposed to different conditions. Metabolomics is applied in many aspects of natural drug discoveries, particularly in bioactivity screening to improve dereplication and identification procedures. Fast dereplication of known compounds and identification of lead bioactive metabolites is important in the primary stages of metabolomics profiling prior to an intensive isolation work. Two levels of metabolomics were used in this study. First was metabolites fingerprinting which aimed for rapid classification of samples by comparing the metabolites patterns or fingerprints. Second was metabolites profiling and dereplication study for class of compounds related to a specific pathway in order to individually identify and quantify these metabolites. This study involved isolation of endophytic fungus Aspergillus aculeatus from Egyptian medicinal plants, Terminalia laxiflora. Identification of the strains has been achieved through molecular biological methods. Metabolomic profiling, using NMR and HR-MS were done at different stages of the growth phase for both solid and liquid culture media. Dereplication studies were accomplished by utilizing the MZmine 2.10 software with aid of the AntiBase and DNP databases. By end of the dereplication process metabolites were sorted out into three levels; level 1: identified compounds, level 2: putatively annotated compound class and level 3: completely unidentified and unclassified compounds. Multivariate data analysis was employed by using PCA in order to classify samples into groups, trends and outliers, which maximize the information, can be obtained from spectral data. OPLS-DA was used to correlate the chemical profile with tested biological activity. Metabolomics has been shown to be a powerful facilitator in the discovery of natural products, which are considered an excellent source for novel leads