Anti-infective nitazoxanide disrupts transcription of ribosome biogenesis-related genes in yeast

Siyu Xu,Naomichi Yamamoto 한국유전학회 2020 Genes & Genomics Vol.42 No.8

Background Nitazoxanide is a broad-spectrum, anti-parasitic, anti-protozoal, anti-viral drug, whose mechanisms of action have remained elusive. Objective In this study, we aimed to provide insight into the mechanisms of action of nitazoxanide and the related eukaryotic host responses by characterizing transcriptome profiles of Saccharomyces cerevisiae exposed to nitazoxanide. Methods RNA-Seq was used to investigate the transcriptome profiles of three strains of S. cerevisiae with dsRNA virus-like elements, including a strain that hosts M28 encoding the toxic protein K28. From the strain with M28, an additional substrain was prepared by excluding M28 using a nitazoxanide treatment. Results Our transcriptome analysis revealed the effects of nitazoxanide on ribosome biogenesis. Many genes related to the UTP A, UTP B, Mpp10-Imp3-Imp4, and Box C/D snoRNP complexes were differentially regulated by nitazoxanide exposure in all of the four tested strains/sub-strains. Examples of the differentially regulated genes included UTP14, UTP4, NOP4, UTP21, UTP6, and IMP3. The comparison between the M28-laden and non-M28-laden sub-strains showed that the mitotic cell cycle was more significantly affected by nitazoxanide exposure in the non-M28-laden sub-strain. Conclusions Overall, our study reveals that nitazoxanide disrupts regulation of ribosome biogenesis-related genes in yeast.

mRNA-Seq reveals accumulation followed by reduction of small nuclear and nucleolar RNAs in yeast exposed to antiviral ribavirin

Xu, Siyu,Yamamoto, Naomichi ELSEVIER 2017 FEMS YEAST RESEARCH Vol.17 No.7

Effects of the biocides on the culturable house dust-borne bacterial compositions and diversities

Xu, Siyu,An, Choa,Kim, Songha,Lee, Seungeun,Lee, Kiyoung,Yamamoto, Naomichi Informa UK (TaylorFrancis) 2016 Human and ecological risk assessment Vol.22 No.5

<P>Biocides are used ubiquitously in indoor environments, but knowledge is limited about how they impact indoor bacterial compositions and diversities. In this study, an in vitro experiment was conducted to demonstrate changes in the culturable house dust-borne bacterial compositions and diversities by exposures to three biocides of CuSO4 (CUS), triclosan (TRC), or benzalkonium chloride with respective concentrations of 90, 45, and 0.1g ml(-1). The high-throughput sequencing was used to characterize the bacterial compositions and diversities. The diversity analysis showed reductions in the species richness and evenness by exposures to CUS and TRC (p < 0.05, Wilcoxon signed rank tests). The diversity analysis revealed the significant changes in the community memberships for CUS and TRC (p < 0.05, P-tests based on the Jaccard indices), which were thought due to selective bacterial inhibitions. The taxonomic analysis found the inhibitions of Enterococcus, Peptoniphilus, Anaerococcus, Finegoldia,Clostridium sensu stricto, and Stenotrophomonas. The findings of the present in vitro study provide important insights into how use of biocides in indoor environments affects bacterial compositions and diversities. Future in situ research is warranted to confirm how they impact indoor microbial compositions and diversities, which are thought to be important for human health.</P>

Non-isothermal Decomposition Kinetics of a New High-energy Organic Potassium Salt: K(DNDZ)

Xu, Kangzhen,Zhao, Fengqi,Song, Jirong,Ren, Xiaolei,Gao, Hongxu,Xu, Siyu,Hu, Rongzu Korean Chemical Society 2009 Bulletin of the Korean Chemical Society Vol.30 No.10

A new high-energy organic potassium salt, 2-(dinitromethylene)-1,3-diazepentane potassium salt K(DNDZ), was synthesized by reacting of 2-(dinitromethylene)-1,3-diazepentane (DNDZ) and potassium hydroxide. The thermal behavior and non-isothermal decomposition kinetics of K(DNDZ) were studied with DSC, TG/DTG methods. The kinetic equation is $\frac{d{\alpha}}{dT}$ = $\frac{10^{13.92}}{\beta}$3(1 - $\alpha$[-ln(1 - $\alpha$)]$^{\frac{2}{3}}$ exp(-1.52 ${\times}\;10^5$ / RT). The critical temperature of thermal explosion of K(DNDZ) is $208.63\;{^{\circ}C}$. The specific heat capacity of K(DNDZ) was determined with a micro-DSC method, and the molar heat capacity is 224.63 J $mol^{-1}\;K^{-1}$ at 298.15 K. Adiabatic time-to-explosion of K(DNDZ) obtained is 157.96 s.

Non-isothermal Decomposition Kinetics of a New High-energy Organic Potassium Salt: K(DNDZ)

Kangzhen Xu,Xiaolei Ren,Fengqi Zhao,Hongxu Gao,Siyu Xu,Rongzu Hu,Jirong Song 대한화학회 2009 Bulletin of the Korean Chemical Society Vol.30 No.10

A new high-energy organic potassium salt, 2-(dinitromethylene)-1,3-diazepentane potassium salt K(DNDZ), was synthesized by reacting of 2-(dinitromethylene)-1,3-diazepentane (DNDZ) and potassium hydroxide. The thermal behavior and non-isothermal decomposition kinetics of K(DNDZ) were studied with DSC, TG/DTG methods. The kinetic equation is d 1013.92 3(1 ) dT ααβ= −2[−ln(1 − α )]3 exp(−1.52 × 105 / RT). The critical temperature of thermal explosion of K(DNDZ) is 208.63 oC. The specific heat capacity of K(DNDZ) was determined with a micro-DSC method, and the molar heat capacity is 224.63 J mol‒1 K‒1 at 298.15 K. Adiabatic time-to-explosion of K(DNDZ) obtained is 157.96 s.

Extended Gradient-based Iterative Algorithm for Bilinear State-space Systems with Moving Average Noises by Using the Filtering Technique

Siyu Liu,Yanliang Zhang,Ling Xu,Feng Ding,Ahmed Alsaedi,Tasawar Hayat 제어·로봇·시스템학회 2021 International Journal of Control, Automation, and Vol.19 No.4

This paper develops a filtering-based iterative algorithm for the combined parameter and state estimationproblems of bilinear state-space systems, taking account of the moving average noise. In order to deal with thecorrelated noise and unknown states in the parameter estimation, a filter is chosen to filter the input-output datadisturbed by colored noise and a Kalman state observer (KSO) is designed to estimate the states by minimizing thetrace of the error covariance matrix. Then, a KSO extended gradient-based iterative (KSO-EGI) algorithm and afiltering based KSO-EGI algorithm are presented to estimate the unknown states and unknown parameters jointlyby the iterative estimation idea. The simulation results demonstrate the effectiveness of the proposed algorithms.

Aerodynamic performance of high-lift blades in low-pressure turbines with periodic upstream wakes

Siyu Yang,Baopeng Xu,Fu Tian,Bin Wang 대한기계학회 2023 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.37 No.5

The aerodynamic performance of high-lift blades was experimentally investigated at different Reynolds numbers ranging from 0.8×10 5 to 1.8×10 5 . Upstream wakes, inherent in real aero-engines, were generated by moving bars operating at reduced frequencies (Fr) of 0.3 and 0.6. Measurements were carried out by pneumatic probes and static pressure taps on the blade surfaces. The results show that high-lift blades experience a significant rise in profile loss under steady conditions, which is mitigated by upstream wakes due to the suppressed separation bubble. The loading distributions relate the non-dimensional flow deceleration rate (DR) to the profile loss. It is found that the variation pattern depends on the flow state, which is classified into parabolic increase, linear increase, and concave parabolic variation. A single hot-wire probe was employed to measure the boundary layer at the trailing edge. The results are used to examine the modified loss model based on Denton’s method.

Taxonomic diversity of fungi deposited from the atmosphere

Woo, Cheolwoon,An, Choa,Xu, Siyu,Yi, Seung-Muk,Yamamoto, Naomichi Nature Publishing Group UK 2018 The ISME journal Vol.12 No.8

<P>Fungi release spores into the global atmosphere. The emitted spores are deposited to the surface of the Earth by sedimentation (dry deposition) and precipitation (wet deposition), and therefore contribute to the global cycling of substances. However, knowledge is scarce regarding the diversities of fungi deposited from the atmosphere. Here, an automatic dry and wet deposition sampler and high-throughput sequencing plus quantitative PCR were used to observe taxonomic diversities and flux densities of atmospheric fungal deposition. Taxon-specific fungal deposition velocities and aerodynamic diameters (<I>d</I><SUB>a</SUB>) were determined using a collocated cascade impactor for volumetric, particle-size-resolved air sampling. Large multicellular spore-producing dothideomycetes (<I>d</I><SUB>a</SUB> ≥ 10.0 μm) were predominant in dry deposition, with a mean velocity of 0.80 cm s<SUP>–1</SUP> for all fungal taxa combined. Higher taxonomic richness was observed in fungal assemblages in wet deposition than in dry deposition, suggesting the presence of fungal taxa that are deposited only in wet form. In wet deposition, agaricomycetes, including mushroom-forming fungi, and sordariomycetes, including plant pathogenic species, were enriched, indicating that such fungal spores serve as nuclei in clouds, and/or are discharged preferentially during precipitation. Moreover, this study confirmed that fungal assemblage memberships and structures were significantly different between dry and wet deposition (<I>P</I>-test, <I>p</I> <I><</I> 0.001). Overall, these findings suggest taxon-specific involvement of fungi in precipitation, and provide important insights into potential links between environmental changes that can disturb regional microbial communities (e.g., deforestation) and changes in precipitation patterns that might be mediated by changes in microbial communities in the atmosphere.</P>

Comparison of fecal microbiota of three captive carnivore species inhabiting Korea

AN, Choa,OKAMOTO, Yumiko,XU, Siyu,EO, Kyung Yeon,KIMURA, Junpei,YAMAMOTO, Naomichi JAPANESE SOCIETY OF VETERINARY SCIENCE 2017 The Journal of veterinary medical science Vol.79 No.3

<P>This study aimed at characterizing fecal microbiota of three captive carnivore species of leopard cats <I>Prionailurus bengalensis</I>, Eurasian otters <I>Lutra lutra</I> and raccoon dogs <I>Nyctereutes procyonoides</I>. We used DNA barcoding sequencing to analyze 16S rRNA genes of uncultured bacteria in the feces collected in the Seoul Zoo. The sequencing analyses revealed that: 1) Firmicutes was the most dominant phylum for all three animals; 2) bacterial genus-rank compositions were distinct across species of the animals; and 3) bacterial community memberships were different across species of the studied animals. We expect such baseline information is useful for better understanding of these endangered species and future management of their health in zoos.</P>

Optimization of Anthraquinone Dyes Decolorization Conditions with Response Surface Methodology by Aspergillus

( Yufeng Ge ),( Bin Wei ),( Siyu Wang ),( Zhiguo Guo ),( Xiaolin Xu ) 한국화학공학회 2015 Korean Chemical Engineering Research(HWAHAK KONGHA Vol.53 No.3

A large amount of dye wastewater poses a threat to environmental safety. Disperse blue, an anthraquinone dye that is widely used in textile dyes, is difficult to degrade in wastewater. In this work, one fungus was screened according to the decolorization rate of disperse blue. The fungus was identified and named Aspergillus XJ-2 on the basis of its morphological characteristics and 18s rDNA. Response surface method was used to optimize culture conditions for A. XJ-2. The optimum values of obtained responses were as follows: temperature, 35 °C; pH, 5.2; carbon-to nitrogen ratio, 30:5.5; and rotation ratio, 175 r·min-1. Under optimized conditions, the decolorization rate of A. XJ-2 was up to 94.8% in 48 h.