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Various histone purification and in vitro chromatin reconstitution for the study of biophysical properties with magnetic tweezers assay
Get PDFDepartment of Biological SciencesEukaryotic DNA has a compacted high-ordered structure, known as chromatin. The fundamental units of chromatin are nucleosomes, which consist of DNA and histone proteins. Chromatin structure has many biological functions. For instance, chromatin protects DNA from damaging factors. DNA metabolism such as transcription and DNA repair is also regulated by chromatin structure. In addition, histone tail regions are targets for post-translational modification, which is associated with epigenetic control of DNA metabolism. In this paper, I purified all canonical Xenopus laevis core histone proteins in E. coli system with a milligram scale. Histone octamer was well assembled with dialysis and purified as size exclusion in vitro condition. Then, a single nucleosome was successfully reconstituted in vitro. Nucleosome reconstitution was confirmed with electrophoretic shift assay and micrococcal nuclease assay. Multiple nucleosomes were also reconstituted with multiple Widom 601 sequences, which have high binding affinity to histone octamer, in vitro. To investigate the tail effect on nucleosome stability, histones, in which tail region is deleted, were generated using mutagenesis. The tailless histone was overexpressed in E. coli system and purified using size exclusion and ion-exchange chromatographic techniques, successively. Purified tailless histones can be still reconstituted into nucleosomes. Magnetic tweezers technique is one of the single molecule techniques to characterize the physical properties of DNA molecules. The multiple-nucleosome formation was confirmed using magnetic tweezers. With the method of this paper, in vitro multiple tailless nucleosomes will be able to reconstitute. In this case, it will be the key to histone tail effects research in vitro with magnetic tweezers. The undisclosed mechanism of some histone chaperones can be revealed with in vitro chromatin reconstitution and single molecule techniques.ope
Effects of pulse-like ground motions and wavelet asymmetry on responses of cantilever retaining wall
No full textFault-rupture processes produce pulse-like ground motions in near-fault regions. These motions are characterized as large-amplitude long-period pulsing that can cause severe structural damage. This study investigates their effect on cantilever retaining wall responses through finite-difference-based numerical simulations. We collect a suite of large-amplitude ground motions which are classified into pulse-like, non-pulse-like, and ambiguous using a pulse indicator. It turns out that relative wall movements by pulse-and non-pulse-like motions are not particularly different. Instead, relative wall movement is highly affected by ground motion Arias intensity, regardless of motion type. Additional simulations using original and reversed ground motion assess the effect of wavelet asymmetry (the ratio of peak amplitudes or energy values in wavelet positive and negative directions) on the wall response. Ground motion asymmetric to the wall movement direction generates larger wall displacement than ground motion asymmetric opposite to the wall movement direction. Relative wall displacements differ by up to approximately 46% depending on the direction of ground motion against the wall movement
Chemical engineering of electrospun nanofibrous-based three-layered nonwoven polymeric protective mask for enhanced performance
No full textDuring the COVID-19 pandemic, face masks, respirators, and personal protective equipment have become common preventive measures. However, the COVID-19 pandemic has highlighted the lack of efficient and reusable face masks worldwide. Immense efforts have been dedicated to designing antidust and antidroplet masks to ensure safe breathing. In this context, electrospun nanofibrous layers have attracted considerable attention for the fabrication of antidust and antidroplet masks. During long-term usage, water droplet layers can lead to pore blockages; this remains a major concern. In this study, a three-layered sandwich structure comprising a hydrophilic spongy layer, hydrophobic support layer, and antidroplet layer was developed to address this concern. Specifically, the structure comprised polyvinylidene fluoride-silica nanoparticles-perfluorooctyl trichlorosilane/polyethylene/polybenzimidazole (PVDF-Si-NPs-PFTOS/PET/PBI) electrospun nanofibrous layers. The PBI layer was utilized as soft, hydrophilic, skin-friendly layer, as supported by the PET layer for better mechanical stability. In addition, PVDF coated with micro-nano scale Si-NPs as modified with a PFTOS nonwoven electrospun layer was used for the antifouling, antidroplet, and splash resistance capabilities. This novel electrospun nanofibrous nonwoven three-layered sandwich structure (PVDF-Si-PFTOS/PET/PBI) exhibited high performance, with competitive antidroplet abilities. Accordingly, this research can be used to fabricate face masks with antidroplet and splash resistance for personal safety and protective equipment
3D-Printed Structural Supercapacitor with MXene-N@Zn-Co Selenide Nanowire Based Woven Carbon Fiber Electrodes
No full textThis work describes the development of a woven carbon fiber and thermoset polyester resin based structural supercapacitor via three-dimensional (3D) printing. The specific surface area and capacitance of the electrodes were increased by hydrothermally synthesized N-doped Zn-Co selenide nanowires on the surface. The supercapacitor with N@ZnCoSe2-MXene exhibited an energy of 2.69 Wh kg-1, a power density of 43.20 W kg-1, and a Coulombic efficiency of 88.8% at 1000 mA g-1 of current density. The cyclic stability and multifunctionality of the device were satisfactory, and the capacitance retention was 83.7% at the same current density after 6000 consecutive charge-discharge cycles. The device's high tensile strength (637.679 MPa) and modulus (36.92 GPa), with an impact energy absorption capacity of 2.22 J g-1, indicated its mechanical robustness. The device exhibits a comparable performance under various weather conditions. It retains 39.11 F g-1 of specific capacitance, 4.62 Wh kg-1 of energy, and 67.29 W kg-1 of power density at 70 degrees C, while it retains 7.87 F g-1 of specific capacitance, 1.78 Wh kg-1 of energy, and 20.98 W kg-1 of power density at -5 degrees C
A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp. paratuberculosis in Cattle
No full textAlthough Mycobacterium avium subsp. paratuberculosis (MAP) has threatened public health and the livestock industry, the current diagnostic tools (e.g., fecal PCR and enzyme-linked immunosorbent assay [ELISA]) for MAP infection have some limitations, such as inconsistent results due to intermittent bacterial shedding or low sensitivity during the early stage of infection. Therefore, this study aimed to develop a novel biomarker focusing on elucidating the gut microbial signature of MAP-positive ruminants, since the clinical signs of MAP infection are closely related to dysbiosis. 16S rRNA-based gut microbial community analysis revealed both a decrease in microbial diversity and the emergence of several distinct taxa following MAP infection. To determine the discriminant taxa diagnostic of MAP infection, machine learning-based feature selection and predictive model construction were applied to taxon abundance data or their transformed derivatives. The selected taxa, such as Clostridioides (formerly Clostridium) difficile, were used to build models using a support vector machine, linear support vector classification, k-nearest neighbor, and random forest with 10-fold cross-validation. The receiver operating characteristic-area under the curve (ROC-AUC) analysis of the models revealed their high accuracy, up to approximately 96%. Collectively, taxonomic signatures of cattle gut microbiotas according to MAP infection status could be identified by feature selection tools and applied to establish a predictive model for the infection state.IMPORTANCE Due to the limitations, such as intermittent bacterial shedding or poor sensitivity, of the current diagnostic tools for Johne's disease, novel biomarkers are urgently needed to aid control of the disease. Here, we explored the fecal microbiota of Johne's disease-affected cattle and tried to discover distinct microbial characteristics which have the potential to be novel noninvasive biomarkers. Through 16S rRNA sequencing and machine learning approaches, a dozen taxa were selected as taxonomic signatures to discriminate the disease state. In addition, when constructing predictive models using relative abundance data of the corresponding taxa, the models showed high accuracy for classification, even including animals with subclinical infection. Thus, our study suggested novel noninvasive microbiological biomarkers that are robustly expressed regardless of subclinical infection and the applicability of machine learning for diagnosis of Johne's disease. Due to the limitations, such as intermittent bacterial shedding or poor sensitivity, of the current diagnostic tools for Johne's disease, novel biomarkers are urgently needed to aid control of the disease. Here, we explored the fecal microbiota of Johne's disease-affected cattle and tried to discover distinct microbial characteristics which have the potential to be novel noninvasive biomarkers
Thermal Transport Property of Quasi 1D S =1 chain NiTe2O5
No full textOne-dimensional magnets are very interesting, although it is well-known that there is no long range-order[1]. Because a spin chain in one-dimensional magnets has the possibility of complex excitations like spinons which have spin-1/2 in chains with S=1/2. Lately, we have reported a quasi-one-dimensional S=1 chain system NiTe2O5[2]. About the crystallographic structural feature of NiTe2O5, NiO6 octahedra are connected to each other through the edge-sharing and the spin(S=1) of each Ni2+ ion at the center of the octahedra forms a quasi-one-dimensional spin chain. By decreasing temperature, spins of Ni2+ ions are ordered as antiferromagnetic long-range order at 30.5 K. The single crystal neutron diffraction reveals the unconventional critical behavior of the order parameter around the ordering temperature. 125Te nuclear magnetic resonance(NMR) experiments exhibit intriguing persistent spin fluctuation above the ordering temperature[3]. More recently, even magnetoelectric(ME) coupling was reported[4]. Thermal transport has been used to probe magnetic systems as an experimental tool in solid-state physics [5]. Because heat transport via the spin system itself and thermal conductivities are influenced by scattering between phonon and magnetic excitations. By using thermal transport, we studied thermodynamic properties associated with these unusual magnetic behaviors in NiTe2O5.
[1] Stephen Blundell, Magnetism in Condensed Matter, Oxford ; New York : Oxford University Press (2001).
[2] Jun Han Lee, Marie Kratochv??lov??, Huibo Cao, Zahra Yamani, JS Kim, Je-Geun Park, GR Stewart, Yoon Seok Oh, Unconventional critical behavior in the quasi-one-dimensional S=1 chain NiTe2O5, Physical Review B 100, 144441 (2019).
[3] Seung-Ho Baek, Jun Han Lee, Yoon Seok Oh, Kwang-Yong Choi, Bernd B??chner, Persistence of Ising-like easy-axis spin correlations in the paramagnetic state of the spin-1 chain compound NiTe2O5, Physical Review B 104, 214431 (2021).
[4] Ajay Tiwari, D. Chandrasekhar Kakarla, G. Macam, C. H. Hsu, F. C. Chuang, H. C. Wu, T. W. Kuo, Arkadeb Pal, H. Chou, D. P. Gulo, H.L. Liu, Y. C. Lai, C. A. Lee, Mitch M. C. Chou, H. D. Yang, Spin-lattice-charge coupling in quasi-one-dimensional spin-chain NiTe2O5, Physical Review Materials 6, 044409 (2022).
[5] A. V. Sologubenko, T. Lorenz, H. R. Ott, A. Freimuth, Thermal conductivity via magnetic excitations in spin-chain materials, J. Low Temp. Phys. 147, 387-403 (2007)
Questioning the South Korean Smart Border: A Critique of Surveillance Racism, Biometric Identity,and Anti-Immigration
No full textThis paper examines the border as an assemblage of surveillance technologies that exert a contentious claim to algorithmic accuracy based on race-embedded biometric data processing. I offer the term surveillance racism???a regime of normalization in which the technical reification of race for the biometric database configures anti-migration and anti-refugee discourses for the well-being of a population or nation. I put forward the border as a biopolitical enclosure in which biometric monitoring through security and risk calculations of threat to the state generates, propagates, and maintains discourses of racism. A discussion of South Korea???s Integrated Border Management System uncovers the workings of a biopolitical enclosure that is committed to constructing a claim about the survival of the Korean nation pitted against the peculiar racial category of unhealthy immigrants from non-Western, developing countries
Magnetic Skyrmion Transistor Gated with Voltage-Controlled Magnetic Anisotropy
No full textThe paradigm shift of information carriers from charge to spin has long been awaited in modern electronics. The invention of the spin-information transistor is expected to be an essential building block for the future development of spintronics. Here, a proof-of-concept experiment of a magnetic skyrmion transistor working at room temperature, which has never been demonstrated experimentally, is introduced. With the spatially uniform control of magnetic anisotropy, the shape and topology of a skyrmion when passing the controlled area can be maintained. The findings will open a new route toward the design and realization of skyrmion-based spintronic devices in the near future
