An Antioxidant Defense System in Radiation-Resistant Bacterium <em>Deinococcus geothermalis</em> against Oxidative Stress

A radiation-resistant bacterium, Deinococcus geothermalis has various stress response mechanisms, including antioxidation. Features that maintain vitality at high radiation doses include the following: enzymatic scavengers of ROS such as catalase, SOD, and peroxidase; strain-specific DNA repair systems such as Deinococcal unique proteins; non-enzymatic responses such as manganese complexes, carotenoids, and DNA-binding proteins. This chapter summarizes the primary response mechanism by redox balance centered on the cystine transporter. It also reviews action characteristics of DNA-binding protein Dps and a putative LysR family protein, and effects on loss of function of the carotenoid biosynthesis genes by transposition of insertion sequences. Environmental adaptation and molecular evolution of radiation-resistant bacterium are also considered to explain the potentials of molecular behavior induced by oxidative stress

Acquisition of Streptomycin Resistance by Oxidative Stress Induced by Hydrogen Peroxide in Radiation-Resistant Bacterium Deinococcus geothermalis

Streptomycin is used primarily to treat bacterial infections, including brucellosis, plague, and tuberculosis. Streptomycin resistance easily develops in numerous bacteria through the inhibition of antibiotic transfer, the production of aminoglycoside-modifying enzymes, or mutations in ribosomal components with clinical doses of streptomycin treatment. (1) Background: A transposable insertion sequence is one of the mutation agents in bacterial genomes under oxidative stress. (2) Methods: In the radiation-resistant bacterium Deinococcus geothermalis subjected to chronic oxidative stress induced by 20 mM hydrogen peroxide, active transposition of an insertion sequence element and several point mutations in three streptomycin resistance (SmR)-related genes (rsmG, rpsL, and mthA) were identified. (3) Results: ISDge6 of the IS5 family integrated into the rsmG gene (dgeo_2335), called SrsmG, encodes a ribosomal guanosine methyltransferase resulting in streptomycin resistance. In the case of dgeo_2840-disrupted mutant strains (S1 and S2), growth inhibition under antibiotic-free conditions was recovered with increased growth yields in the presence of 50 &micro;g/mL streptomycin due to a streptomycin-dependent (SmD) mutation. These mutants have a predicted proline-to-leucine substitution at the 91st residue of ribosomal protein S12 in the decoding center. (4) Conclusions: Our findings show that the active transposition of a unique IS element under oxidative stress conditions conferred antibiotic resistance through the disruption of rsmG. Furthermore, chronic oxidative stress induced by hydrogen peroxide also induced streptomycin resistance caused by point and frameshift mutations of streptomycin-interacting residues such as K43, K88, and P91 in RpsL and four genes for streptomycin resistance

Context-Aware Link Embedding with Reachability and Flow Centrality Analysis for Accurate Speed Prediction for Large-Scale Traffic Networks

This paper presents a novel method for predicting the traffic speed of the links on large-scale traffic networks. We first analyze how traffic flows in and out of every link through the lowest cost reachable paths. We aggregate the traffic flow conditions of the links on every hop of the inbound and outbound reachable paths to represent the traffic flow dynamics. We compute a new measure called traffic flow centrality (i.e., the Z value) for every link to capture the inherently complex mechanism of the traffic links influencing each other in terms of traffic speed. We combine the features regarding the traffic flow centrality with the external conditions around the links, such as climate and time of day information. We model how these features change over time with recurrent neural networks and infer traffic speed at the subsequent time windows. Our feature representation of the traffic flow for every link remains invariant even when the traffic network changes. Furthermore, we can handle traffic networks with thousands of links. The experiments with the traffic networks in the Seoul metropolitan area in South Korea reveal that our unique ways of embedding the comprehensive spatio-temporal features of links outperform existing solutions

A Novel Bus Arrival Time Prediction Method Based on Spatio-Temporal Flow Centrality Analysis and Deep Learning

This paper presents a method for predicting bus stop arrival times based on a unique approach that extracts the spatio-temporal dynamics of bus flows. Using a new technique called Bus Flow Centrality Analysis (BFC), we obtain the low-dimensional embedding of short-term bus flow patterns in the form of IID (Individual In Degree) and IOD (Individual Out Degree) and TOD (Total Out Degree) at every station in the bus network. The embedding using BFC analysis well captures the characteristics of every individual flow and aggregate pattern. The latent vector returned by the BFC analysis is combined with other essential information such as bus speed, travel time, wait time, dispatch intervals, the distance between stations, seasonality, holiday status, and climate information. We employed a family of recurrent neural networks such as LSTM, GRU, and ALSTM to model how these features change over time and to predict the time the bus takes to reach the next stop in subsequent time windows. We experimented with our solution using logs of bus operations in the Seoul Metropolitan area offered by the Bus Management System (BMS) and the Bus Information System (BIS) of Korea. We predicted arrival times for more than 100 bus routes with a MAPE of 1.19%. This margin of error is 74% lower than the latest work based on ALSTM. We also learned that LSTM performs better than GRU with a 40.5% lower MAPE. This result is even remarkable considering the irregularity in the bus flow patterns and the fact that we did not rely on real-time GPS information. Moreover, our approach scales at a city-wide level by analyzing more than 100 bus routes, while previous studies showed limited experiments on much fewer bus routes

Acquisition of Streptomycin Resistance by Oxidative Stress Induced by Hydrogen Peroxide in Radiation-Resistant Bacterium <i>Deinococcus geothermalis</i>

Streptomycin is used primarily to treat bacterial infections, including brucellosis, plague, and tuberculosis. Streptomycin resistance easily develops in numerous bacteria through the inhibition of antibiotic transfer, the production of aminoglycoside-modifying enzymes, or mutations in ribosomal components with clinical doses of streptomycin treatment. (1) Background: A transposable insertion sequence is one of the mutation agents in bacterial genomes under oxidative stress. (2) Methods: In the radiation-resistant bacterium Deinococcus geothermalis subjected to chronic oxidative stress induced by 20 mM hydrogen peroxide, active transposition of an insertion sequence element and several point mutations in three streptomycin resistance (SmR)-related genes (rsmG, rpsL, and mthA) were identified. (3) Results: ISDge6 of the IS5 family integrated into the rsmG gene (dgeo_2335), called SrsmG, encodes a ribosomal guanosine methyltransferase resulting in streptomycin resistance. In the case of dgeo_2840-disrupted mutant strains (S1 and S2), growth inhibition under antibiotic-free conditions was recovered with increased growth yields in the presence of 50 µg/mL streptomycin due to a streptomycin-dependent (SmD) mutation. These mutants have a predicted proline-to-leucine substitution at the 91st residue of ribosomal protein S12 in the decoding center. (4) Conclusions: Our findings show that the active transposition of a unique IS element under oxidative stress conditions conferred antibiotic resistance through the disruption of rsmG. Furthermore, chronic oxidative stress induced by hydrogen peroxide also induced streptomycin resistance caused by point and frameshift mutations of streptomycin-interacting residues such as K43, K88, and P91 in RpsL and four genes for streptomycin resistance

Transposition of Insertion Sequences was Triggered by Oxidative Stress in Radiation-Resistant Bacterium Deinococcus geothermalis

During an oxidative stress-response assay on a putative Dps-like gene-disrupted &Delta;dgeo_0257 mutant strain of radiation-resistant bacterium Deinococcus geothermalis, a non-pigmented colony was observed among the normal reddish color colonies. This non-pigmented mutant cell subsequently displayed higher sensitivity to H2O2. While carotenoid has a role in protecting as scavenger of reactive oxygen species the reddish wild-type strain from radiation and oxidative stresses, it is hypothesized that the carotenoid biosynthesis pathway has been disrupted in the mutant D. geothermalis cell. Here, we show that, in the non-pigmented mutant cell of interest, phytoene desaturase (Dgeo_0524, crtI), a key enzyme in carotenoid biosynthesis, was interrupted by transposition of an ISDge7 family member insertion sequence (IS) element. RNA-Seq analysis between wild-type and &Delta;dgeo_0257 mutant strains revealed that the expression level of ISDge5 family transposases, but not ISDge7 family members, were substantially up-regulated in the &Delta;dgeo_0257 mutant strain. We revealed that the non-pigmented strain resulted from the genomic integration of ISDge7 family member IS elements, which were also highly up-regulated, particularly following oxidative stress. The transposition path for both transposases is a replicative mode. When exposed to oxidative stress in the absence of the putative DNA binding protein Dgeo_0257, a reddish D. geothermalis strain became non-pigmented. This transformation was facilitated by transposition of an ISDge7 family IS element into a gene encoding a key enzyme of carotenoid biosynthesis. Further, we present evidence of additional active transposition by the ISDge5 family IS elements, a gene that was up-regulated during the stationary phase regardless of the presence of oxidative stress

Highly Self-Healable Polymeric Coating Materials with Enhanced Mechanical Properties Based on the Charge Transfer Complex

Polymeric coating materials (PCMs) are promising candidates for developing next-generation flexible displays. However, PCMs are frequently subjected to external stimuli, making them highly susceptible to repeated damage. Therefore, in this study, a highly self-healing PCM based on a charge transfer complex (CTC) was developed, and its thermal, self-healing, and mechanical properties were examined. The self-healing material demonstrated improved thermal stability, fast self-healing kinetics (1 min), and a high self-healing efficiency (98.1%) via CTC-induced multiple interactions between the polymeric chains. In addition, it eliminated the trade-off between the mechanical strength and self-healing capability that is experienced by typical self-healing materials. The developed PCM achieved excellent self-healing and superior bulk (in-plane) and surface (out-of-plane) mechanical strengths compared to those of conventional engineering plastics such as polyether ether ketone (PEEK), polysulfone (PSU), and polyethersulfone (PES). These remarkable properties are attributed to the unique intermolecular structure resulting from strong CTC interactions. A mechanism for the improved self-healing and mechanical properties was also proposed by comparing the CTC-based self-healing PCMs with a non-CTC-based PCM

Data from: A liquid-like organelle at the root of motile ciliopathy

Motile ciliopathies are characterized by specific defects in cilia beating that result in chronic airway disease, subfertility, ectopic pregnancy, and hydrocephalus. While many patients harbor mutations in the dynein motors that drive cilia beating, the disease also results from mutations in so-called Dynein Axonemal Assembly Factors (DNAAFs) that act in the cytoplasm. The mechanisms of DNAAF action remain poorly defined. Here, we show that DNAAFs concentrate together with axonemal dyneins and chaperones into organelles that form specifically in multiciliated cells, which we term DynAPs, for Dynein Axonemal Particles. These organelles display hallmarks of biomolecular condensates, and remarkably, DynAPs are enriched for the stress granule protein G3bp1, but not for other stress granule proteins or P-body proteins. Finally, we show that both the formation and the liquid-like behaviors of DynAPs are disrupted in a model of motile ciliopathy. These findings provide a unifying cell biological framework for a poorly understood class of human disease genes and add motile ciliopathy to the growing roster of human diseases associated with disrupted biological phase separation