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High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH

Cell 2025年

作者： Zhu, Yanyu Balaji, Ashwin Han, Mengting Andronov, Leonid Roy, Anish R. Wei, Zheng Chen, Crystal Miles, Leanne Cai, Sa Gu, Zhengxi Tse, Ariana Yu, Betty Chentzu Uenaka, Takeshi Lin, Xueqiu Spakowitz, Andrew J. Moerner, W.E. Qi, Lei S. Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Chemistry Stanford University Stanford 94305 CA United States Biophysics PhD Program Stanford University Stanford 94305 CA United States Computational Biology Program Public Health Sciences Division and Translational Data Science IRC Fred Hutchinson Cancer Center Seattle 98109 WA United States Department of Chemical Engineering Stanford University Stanford 94305 CA United States Department of Materials Science and Engineering Stanford University Stanford 94305 CA United States Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology Stanford University School of Medicine Stanford 94305 CA United States Sarafan ChEM-H Stanford University Stanford 94305 CA United States Chan Zuckerberg Biohub San Francisco 94080 CA United States

Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease. © 2025 Elsevier Inc.

关键词： CRISPR imaging DNA communication dynamic tracking enhancer-promoter interaction high-resolution imaging live DNA imaging non-repetitive genome imaging Oligo-LiveFISH polymer modeling primary cell

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An Outlook on the Utilization of Perovskite Films in Photocatalytic and Optoelectronic Devices

An Outlook on the Utilization of Perovskite Films in Photoca...

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2023 Advances in science and Engineering Technology International Conferences, ASET 2023

作者： Alashkar, Adnan Ayoub, Mohamad Ali Al-Alami, Abdul Hai Abdelkareem, Mohammad Ali Olabi, Abdul Ghani Mdallal, Ayman American University of Sharjah Materials Science and Engineering PhD Program Sharjah United Arab Emirates University of Sharjah Sustainable and Renewable Energy Engineering Sharjah United Arab Emirates

ISBN: (纸本)9781665454742

The search for novel multi-functional material has been on the rise for the past decades. These materials ought to possess flexible structures and tunable properties in order to be utilized for a variety of applications. Perovskite materials are predominantly used in solar cell applications due to their broad absorption spectrum, long carrier lifetime, and long transport distance of electrons and holes. Nevertheless, their unique and tunable properties allow for their utilization in a wide range of applications. In this work, a review on the application of perovskite materials in hydrogen production, supercapacitors, and optoelectronic devices is presented. The role of perovskite in the improvement of said applications is investigated, and future outlook and remarks are presented. This paper highlights the potential utilization of perovskite material outside the scope of photoelectric devices and solar cells. © 2023 IEEE.

关键词： Perovskite

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Membrane distillation-crystallization of lithium hydroxide

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Sustainable materials and Technologies 2025年 45卷

作者： Carol González Michelle Quilaqueo Gianni Piaggio Lorena Barros Yurieth M. Quintero Andreina García Humberto Estay Advanced Mining Technology Center (AMTC) University of Chile Av. Tupper 2007 (AMTC Building) Santiago Chile. Materials Science and Process Engineering PhD Program Universidad Tecnológica Metropolitana (UTEM) Ignacio Valdivieso 2409 Santiago 8940577 Chile Mining Engineering Department FCFM Universidad de Chile Av. Tupper 2069 8370451 Santiago Chile

The crystallization of lithium hydroxide by a membrane crystallization process was studied, assessing different operational conditions, such as the temperature of the feed Li brine, the flow rate, and the water activity of the permeate, to determine the effect of these variables on the crystallization process. Results showed good agreement with classical crystallization theory, where larger crystal sizes were obtained for lower supersaturation conditions, such as when operating at 40 °C, a flow rate of 0.6 L/min, and a water activity of 1.0. The mentioned conditions resulted in a lower starting flux, and compared to tests that promote a maximum flux, there is a difference of 58 % between the lowest and highest values. However, crystal size impacted the formation of crystals on the membrane surface, reducing the transmembrane water flux drastically, even reaching similar flux values of approximately 1 kg/m 2 h between all conditions. The induction times indicated that the supersaturation condition values required to start the crystal nucleation ranged between 1.08 and 1.20 for all conditions assessed. The analysis of the membrane surface at the end of each test demonstrated that smaller crystal sizes caused a more detrimental impact on the crystal layer formed in terms of the membrane area blocked. Therefore, lower supersaturation conditions that promote the formation of larger crystals are suggested for the further development of the process, in the perspective of industrial applications, to avoid detrimental fouling formation on the membrane. Besides, the similar water flux values reached in the crystallization step for all operational conditions confirm that a similar membrane area will be required to achieve certain productivity. Hence, the results are promising for defining the best operating conditions of the process with a view to future industrial applications.

关键词： Brines

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Rational Design of Ultrastable Conjugated Microporous Polymers Based on Pyrene and Perylene Units as High-Performance Organic Electrode materials for Supercapacitor Applications

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ACS Applied Energy materials 2023年第15期6卷 8277-8287页

作者： Singh, Poonam Nagendra Mohamed, Mohamed Gamal Chaganti, Swetha V. Sharma, Santosh U. Ejaz, Moshin Lee, Jyh-Tsung Kuo, Shiao-Wei Department of Materials and Optoelectronic Science Center for Functional Polymers and Supramolecular Materials National Sun Yat-Sen University Kaohsiung804 Taiwan Department of Chemistry Faculty of Science Assiut University Assiut71515 Egypt Department of Chemistry National Sun Yat-Sen University Kaohsiung80424 Taiwan International PhD Program for Science National Sun Yat-Sen University Kaohsiung80424 Taiwan Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung807 Taiwan

We successfully synthesized three perylene dianhydride (PDI)-based conjugated microporous polymers (CMPs), namely, Py-Ph-Pery, TPE-Ph-Pery, and TPA-Ph-Pery CMPs, through a Suzuki-Miyaura coupling reaction. The precursors used in the reaction contained brominated compounds of pyrene (Py), tetraphenylethylene (TPE), triphenylamine (TPA), and 1,4-benzeneboronic acid, which were coupled with redox-active PDI unit. To evaluate the thermal stability, molecular structure, and porosity properties of the synthesized CMPs, we conducted an examination of their Brunauer-Emmett-Teller isotherm, along with spectroscopic and microscopic analyses. These CMPs demonstrated moderate thermal stability based on thermogravimetric analysis. In terms of electrochemical performance, the Py-Ph-Pery CMP exhibited a high capacitance of 300 F g-1 (measured at 0.5 A g-1), indicating its excellent capacitive properties. Furthermore, the Py-Ph-Pery CMP displayed exceptional cycle stability at 10 A g-1, retaining more than 93% of its capacity over 5000 cycles. The findings illustrate the potential of these CMPs for reliable and durable energy storage applications. Additionally, we utilized synthesized CMPs to assess the electrochemical characteristics of a symmetric coin supercapacitor. The results further validate the suitability of these CMPs for practical electrical energy storage applications, highlighting their significant promise. © 2023 American Chemical Society.

关键词： Supercapacitor

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Four Examples of Unimolecular Electrical Rectifiers

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Electrochemical Society Interface 2004年第1期13卷 40-44页

作者： Metzger, Robert M. Department of Chemistry Materials Science PhD Program United States Department of Chemistry University of Mississippi United States

The unimolecular electronics (UE) aims to produce molecular electronic devices at 1-2 nm scale to meet the needs of integrated circuits. The UE is advanced by measuring electrical conductivity of single molecules or Langmuir-Blodgett (LB) monolayers. A single molecule is touched by scanning tunneling microscopy (STM) tip, conducting-tip atomic force microscopy (AFM) tip or between two Au tips are measured in parallel by making electrical contacts to sandwiches of organic monolayers. The metal | organic | metal sandwiches are prepared and measured without destroying organic layer.

关键词： Electric rectifiers

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Eclipse timing variations in the WD + dM eclipsing binary RR Cae

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Monthly Notices of the Royal Astronomical Society 2023年第4期523卷 5086-5108页

作者： Rattanamala, R. Awiphan, S. Komonjinda, S. Phriksee, A. Sappankum, P. A-Thano, N. Chitchak, S. Rittipruk, P. Sawangwit, U. Poshyachinda, S. Reichart, D.E. Haislip, J.B. PhD Program in Astronomy Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Physics and General Science Program Faculty of Science and Technology Nakhon Ratchasima Rajabhat University Nakhon Ratchasima30000 Thailand 260 Moo 4 Donkaew Mae Rim Chiang Mai50180 Thailand Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Institute of Astronomy National Tsing Hua University Hsinchu30013 Taiwan Department of Physics Faculty of Science Udon Thani Rajabhat University Udon Thani41000 Thailand Department of Physics and Astronomy University of North Carolina at Chapel Hill Chapel HillNC27599 United States

We present the binary model and the eclipse timing variations of the eclipsing binary RR Cae, which consists of a white dwarf eclipsed by an M-type dwarf companion. The multiwavelength optical photometry from the Transiting Exoplanet Survey Satellite (TESS), the 0.6-m PROMPT-8 telescope, and the 0.7-m Thai Robotic Telescope at Spring Brook Observatory, combined with archive H α radial velocities from the Very Large Telescope (VLT) are analysed. From the data, the physical parameters of the system are obtained along with 430 new times of minima. The TESS light curves in 2018 and 2020 show out-of-eclipse variations, which might be caused by a large spot on the secondary component. The light travel time effect models due to the gravitational interaction of one or two circumbinary objects are adopted to fit the cyclic variations in the RR Cae’s O-C curve. The fitting solution of the O-C curve with one circumbinary object model shows a periodic variation with a period of 16.6 ± 0.2 yr and an amplitude of 14 ± 1 s, which can be caused by a planet with a minimum mass of 3.4 ± 0.2 MJup. When we consider the model with two circumbinary objects, the O-C curve shows cyclic variations with periods of 15.0 ± 0.5 yr and 39 ± 5 yr and amplitudes of 12 ± 1 s and 20 ± 5 s, respectively, corresponding to minimum masses of 3.0 ± 0.3 MJup and 2.7 ± 0.7 MJup © 2023 The Author(s) Published by Oxford University Press on behalf of Royal Astronomical Society.

关键词： Travel time

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The anatomic determinants of conductive hearing loss secondary to tympanic membrane perforation

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Journal of Otology 2017年第3期12卷 125-131页

作者： David J.Carpenter Debara L.Tucci David M.Kaylie Dennis O.Frank-Ito Division of Head and Neck Surgery & Communication Sciences Department of Surgery Duke University Medical Center Durham NC USA Computational Biology & Bioinformatics PhD Program Duke University Durham NC USA Department of Mechanical Engineering and Materials Science Duke University Durham NC USA

Objectives: Recent studies have introduced middle ear volume(MEV) as a novel determinant of perforation-induced conductive hearing loss(CHL) in a mechanism driven by trans-tympanic membrane pressure differences. The primary aims of this preliminary report are to: 1) correlate CHL with perforation size; 2) describe the relationship between CHL and MEV; and 3) compare CHL across a range of cholesteatoma ***: A retrospective pilot study was performed in 31 subjects with audiometry indicative of conductive hearing loss, temporal bone CT scans,and no prior middle ear surgery. Perforation size and MEV were analyzed with respect to CHL in a cohort of 10 perforated ears with no cholesteatoma. CHLs were compared in 3 groups defined by extent of cholesteatoma ***: Ears with large and small perforations showed mean ABG values of 32.0 ± 15.7 dB and 16.0 ± 16.4 dB, respectively. A direct relationship was observed between MEV and CHL for ears with large perforations across all frequencies, whereas this relationship for small perforations was frequency-dependent. Finally, a statistically significant increase in CHL was found across ears with increasing cholesteatoma involvement at 1000 Hz(X^2(2) = 9.786, p = 0.008),2000 Hz(x^2(2) = 8.455, p = 0.015),and 4000 Hz(x^2(2)= 8.253, p = 0.016).Conclusions: These pilot data suggest that greater perforation-induced conductive hearing losses may be associated with larger perforation sizes and cholesteatoma. The correlation between MEV and CHL may require additional study.

关键词： Perforation-induced hearing loss Conductive hearing loss Middle ear volume Three-dimensional volume reconstruction

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Disagreement in middle ear volume estimation between tympanometry and three-dimensional volume reconstruction in the context of tympanic membrane perforation

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Journal of Otology 2017年第2期12卷 74-79页

作者： David J.Carpenter Debara L.Tucci David M.Kaylie Dennis O.Frank-Ito Division of Head and Neck Surgery&Communication Sciences Department of SurgeryDuke University Medical CenterDurhamNCUSA Computational Biology&Bioinformatics PhD Program Duke UniversityDurhamNCUSA Department of Mechanical Engineering and Materials Science Duke UniversityDurhamNCUSA

Introduction: Middle ear volume(MEV) is a clinically relevant parameter across middle ear diseases. MEV values between these techniques have never before been tested for agreement in ears with perforated tympanic membranes(TMs).Methods: Middle ears were identified from 36 patients ranging 18-89 years of age with TM perforations who underwent tympanometry and temporal bone computed tomography(CT) between 2005 and 2015. MEVs calculated by both tympanometry and three-dimensional volume reconstruction(3DVR) were analyzed for agreement using Bland Altman plots. The differences between tympanometric and 3DVR MEV values for each given middle ear were characterized across MEV quartiles(1= smallest; 4= largest) and across increasing states of middle ear disease using Kruskale Wallis and Wilcoxon testing with Bonferroni ***: Bland Altman plots demonstrated significant disagreement between MEV measurement techniques. Differences between tympanometric(T) and 3DVR MEV values were significantly greater with increasing average(i.e.(Tt3DVR)/2)) MEV per linear regression(p < 0.0001). Significance was demonstrated between fourth and first average MEV quartiles(p= 0.0024), fourth and second quartiles(p= 0.0024), third and first quartiles(p= 0.0048), and third and second quartiles(p= 0.048). Absolute MEV difference was not significantly different across varying states of middle ear disease(p= 0.44).Conclusion: Statistically and clinically significant disagreement was demonstrated between tympanometric and 3DVR MEV values. Studies that vary in MEV estimation techniques may be expected to demonstrate significantly different results. These preliminary results suggest that clinicians should endeavor to seek further confirmation when interpreting high tympanometric MEV values.

关键词： Middle ear volume Tympanometry Three-dimensional volume reconstruction Tympanic membrane perforation

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Period variation of an eclipsing binary system BQ Ari 17

Period variation of an eclipsing binary system BQ Ari

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17th Siam Physics Congress: Carbon Neutrality, SPC 2022

作者： Rattanamala, R. Komonjinda, S. Awiphan, S. Wutsang, S. Sappankum, P. Deesuan, L. Department of Physics and General Science Faculty of Science and Technology Nakhon Ratchasima Rajabhat University Nakhon Ratchasima30000 Thailand PhD Program in Astronomy Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Department of Physics and Materials Science Faculty of Science Chiang Mai University Chiang Mai50200 Thailand 260 Moo 4 Donkaew Mae Rim Chiang Mai50180 Thailand

This study was aimed to study the period variation of the eclipsing binary BQ Ari. The system was observed from Thai Robotic Telescope at Spring Brook Observatory (TRT-SBO) between 2019 and 2020, Regional Observatory for Public, Chachoengsao (ROP-CCO) in 2021, and Transiting Exoplanet Survey Satellite (TESS) in Sector 42 and 43. The data obtained were used to create the light curves in each wavelength and compute the times of minima. As the result, we receive 311 time of minima. We combined the time of minima from the previously published with our values to calculate the O - C diagram. The O - C diagram shown the period variation with a period about 6-8 years and amplitude about 0.0020 days. The possibility of the period variation of BQ Ari may be due to the third body component with the mass of 0.0948 M o (M dwarf) and the orbital separation (a 3sini) around 3.96 AU. © Published under licence by IOP Publishing Ltd.

关键词： Observatories

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An ultraefficient surface functionalized Ti3C2Tx MXene piezocatalyst: synchronous hydrogen evolution and wastewater treatment

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Journal of materials Chemistry A 2023年第6期12卷 3340-3351页

作者： Lai, Sz-Nian Chen, Winston Yenyu Yen, Chao-Chun Liao, Yin-Song Chen, Po-Han Stanciu, Lia Wu, Jyh Ming Department of Materials Science and Engineering National Tsing Hua University 101 Section 2 Kuang Fu Road Hsinchu300 Taiwan PhD Program in Prospective Functional Materials Industry National Tsing Hua University 101 Section 2 Kuang Fu Road Hsinchu300 Taiwan High Entropy Materials Center National Tsing Hua University 101 Section 2 Kuang Fu Road Hsinchu300 Taiwan Tsing Hua Interdisciplinary Program National Tsing Hua University 101 Section 2 Kuang Fu Road Hsinchu300 Taiwan School of Materials Engineering Purdue University 610 Purdue Mall West LafayetteIN47907 United States Department of Materials Science and Engineering National Chung Hsing University 145 Xingda Road Taichung402 Taiwan

The Ti3C2Tx surface contains hydroxyl groups that can be modified through self-assembled monolayers by using (3-chloropropyl) trimethoxysilane (CPTMS) and fluoroalkylsilane (FOTS). This study demonstrates that an ultrahigh level of piezoelectricity can be achieved by modifying the Si-O bond of organo-silane headgroups in Ti3C2Tx. The theoretical calculation of surface functionalized Ti3C2Tx-FOTS reveals that its Si-O bond causes localized lattice distortion and enhances the noncentrosymmetric structure on the Ti3C2Tx surface. Ti3C2Tx-FOTS exhibits significantly higher butterfly loops than pristine Ti3C2Tx. The calculated rate constant of Ti3C2Tx-FOTS for dye degradation was 0.9 min−1, 15-fold higher than that of Ti3C2Tx-CPTMS and 111-fold higher than that of pristine Ti3C2Tx. The hydrogen evolution rate of Ti3C2Tx-FOTS is 900.46 μmo1 g−1 h−1, three times higher than that of Ti3C2Tx. The bifunctional surface functionalized Ti3C2Tx-FOTS can simultaneously catalyse the hydrogen evolution reaction (HER) and decomposition of wastewater, demonstrating that Ti3C2Tx-FOTS, obtained through the surface engineering of Ti3C2Tx, is a superior piezocatalyst. © 2024 The Royal Society of Chemistry.

关键词： Rate constants

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