Article
Chemistry, Multidisciplinary
Jaehun Yi, Sanghun Yeou, Nam Ki Lee
Summary: This study reveals that DNA bending force facilitates the formation of Z-DNA, and increasing bending force leads to more Z-DNA formation. The bending force affects the Mg2+ concentration threshold for B-Z transition, lowering it. Monte Carlo simulations suggest that the B-Z transition stabilizes the bent DNA conformation through the formation of B-Z junction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Madhabi M. Bhanjadeo, Partha S. Nial, Chakkarai Sathyaseelan, Ajit K. Singh, Juhi Dutta, Thenmalarchelvi Rathinavelan, Umakanta Subudhi
Summary: The transition from right-handed to left-handed DNA not only plays a controlling role in gene expression switching but also has importance in nanomechanical device design. This study demonstrates that LaCl3 can induce controlled and reversible B-Z transition in short repeat sequences, providing insights into the molecular mechanism of this transition. The binding of LaCl3 to the phosphate backbone of Z-DNA is strong, resulting in the irreversible thermal melting of LaCl3-induced Z-DNA. These findings suggest that LaCl3 can be used as an inducer of left-handed DNA in other short oligonucleotide sequences.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biology
Dmitry Umerenkov, Alan Herbert, Dmitrii Konovalov, Anna Danilova, Nazar Beknazarov, Vladimir Kokh, Aleksandr Fedorov, Maria Poptsova
Summary: Using the DNABERT transformer algorithm trained on experimentally identified Z-DNA forming sequences (Z-flipons), we performed genome-wide interrogation and obtained significant improvements over existing approaches. Z-flipons were found to be enriched in promoters and telomeres, overlapping with genetic loci related to RNA expression, editing, splicing, and disease-associated variants. Our findings also suggest a potential role of Z-RNA in mediating these effects.
LIFE SCIENCE ALLIANCE
(2023)
Article
Chemistry, Multidisciplinary
Chak Kui Wong, Jonathan P. K. Doye
Summary: Molecular simulations using coarse-grained models provide insights into the structure, dynamics, and mechanics of DNA origamis. In this study, the focus is on the free-energy landscape of a jointed DNA origami, where the predicted results differ from experimental observations, possibly due to assembly defects affecting the ensemble of structures.
APPLIED SCIENCES-BASEL
(2022)
Article
Environmental Studies
Belen Perez Perez, Pilar Diaz-Cuevas
Summary: This study analyzes the relationship between water and renewable energy in the Monachil river valley and its social acceptance in terms of territory and landscape. The study finds that water is an integral part of the valley's territorial identity and landscape, with a strong link to hydroelectric power. Recently, solar energy has led to a local energy transition in Monachil.
Article
Biochemistry & Molecular Biology
Sook Ho Kim, Hae Jun Jung, Seok-Cheol Hong
Summary: Methylcytosines in mammalian genomes play a crucial role in gene regulation and are implicated in various diseases, including cancer. A new optical technique has been developed to characterize the activity of DNA methyltransferases (DMT) and the effects of inhibitors, offering a more direct and sensitive approach without the need for amplification steps or methylation-sensitive nucleases. This method has shown promise in evaluating the inhibitory effects of natural bio-active compounds on DMT, providing a potential avenue for the development of DMT-related anticancer drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Bo Zheng, Xiao-Long Liu, Rong Fan, Jian Bai, Hao Wen, Lu-Tao Du, Guo-Qing Jiang, Chun-Ying Wang, Xiao-Tang Fan, Yi-Nong Ye, Yun-Song Qian, Ying-Chao Wang, Gao-Jing Liu, Guo-Hong Deng, Feng Shen, He-Ping Hu, Hui Wang, Qing-Zheng Zhang, Lan-Lan Ru, Jing Zhang, Yan-Hang Gao, Jie Xia, Hua-Dong Yan, Min-Feng Liang, Yan-Long Yu, Fu-Ming Sun, Yu-Jing Gao, Jian Sun, Chun-Xiu Zhong, Yin Wang, Fei Kong, Jin-Ming Chen, Dan Zheng, Yuan Yang, Chuan-Xin Wang, Lin Wu, Jin-Lin Hou, Jing-Feng Liu, Hong-Yang Wang, Lei Chen
Summary: This study investigated HBV integration and mutation landscapes on cfDNA, revealing a positive correlation between ctDNA concentration and detection rate of integration hotspots. The origin of HBV integrations in cfDNA was traced back to tumor tissue through whole-genome sequencing. Identification of a potential HCC-related mutational hot zone provided valuable insights into noninvasive virus insertion/mutation detection possibilities.
CLINICAL CANCER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
John R. Buzzo, Aishwarya Devaraj, Erin S. Gloag, Joseph A. Jurcisek, Frank Robledo-Avila, Theresa Kesler, Kathryn Wilbanks, Lauren Mashburn-Warren, Sabarathnam Balu, Joseph Wickham, Laura A. Novotny, Paul Stoodley, Lauren O. Bakaletz, Steven D. Goodman
Summary: Biofilms formed by bacteria rely on a rare Z-form DNA structure containing eDNA and DNABII proteins for structural integrity. Stabilization of Z-DNA by DNABII proteins promotes biofilm formation and stability, while disruption of Z-DNA structure can disturb existing biofilms. The universal bacterial DNABII family of proteins is shown to stabilize both bacterial and host eDNA in the Z-form, suggesting a role in biofilm pathogenesis and immune interactions.
Article
Biochemistry & Molecular Biology
Sook Ho Kim, Hae Jun Jung, Il-Buem Lee, Nam-Kyung Lee, Seok-Cheol Hong
Summary: This study investigated the impact of specific DNA sequences on Z-DNA formation, revealing the influence of different repeat sequences on the thermodynamic and kinetic features of Z-DNA formation. TG repeat sequences are advantageous for Z-DNA in terms of torsion and bubble selection, while CG repeat sequences likely act as torsion absorbers.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yu-Cheng Liu, Dah-Yen Yang, Sheh-Yi Sheu
Summary: G-quadruplexes have become attractive drug targets in cancer therapy, but the polymorphic nature of their structures makes understanding their conformational conversion mechanisms challenging. This study used molecular dynamics simulation to show that as salt concentration increases, the mechanism of conformational conversion shifts from multi-pathway to sequential pathways, with conformational conversion being more feasible upon K+ binding compared to Na+ binding in high-salt solutions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Diane M. Spencer, Angel Garza Reyna, David S. Pisetsky
Summary: DNA can have different backbone conformations, with Z-DNA being a left-handed helix with a zig-zag orientation depending on base sequence, modification, and supercoiling. Experimental results demonstrate that anti-Z-DNA antibodies can serve as probes for detecting the presence of Z-DNA in DNA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Mathematics, Applied
Andrew Cleary, Jacob Page
Summary: This paper presents a new method for systematically exploring the free-energy landscape in the study of superfluids. It discovers new equilibrium states and evaluates the likelihood of observing certain states in experiments. Additionally, it investigates the dynamics near the minimizing state.
Article
Chemistry, Multidisciplinary
Swantje Mohr, Jagannath Jana, Yoanes Maria Vianney, Klaus Weisz
Summary: Canonical G-quadruplexes can have diverse topologies based on the arrangement of loops connecting the G-columns, with a novel intramolecular G-quadruplex structure resulting from a change in the last G-tract of a three-layered fold. The newly formed (3+1) hybrid fold may offer potential applications in quadruplex-based technologies.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Economics
Lanka Horstink, Julia M. Wittmayer, Kiat Ng
Summary: To achieve the EU's goal of providing 'Clean Energy for All Europeans', a shift from centralized, fossil-fuel based systems to decentralized systems based on renewable energy sources is envisioned, with a focus on citizen participation. This paper categorizes collective social actors that produce and consume energy from renewable sources, aiming to clarify their role in the energy landscape and recommend policy adjustments to support the implementation of clean energy policies.
Article
Crystallography
Thierry Prange, Nathalie Colloc'h, Anne-Claire Dhaussy, Marc Lecouvey, Evelyne Migianu-Griffoni, Eric Girard
Summary: Single crystals of B-DNA and Z-DNA oligomers were studied under high hydrostatic pressure and compared to A-DNA crystals. The amplitude of base compression was found to be higher for Z-DNA and highest for B-DNA. B-DNA crystals degraded rapidly around 400-500 MPa, while the Z-DNA structure showed greater resistance up to 1.2 GPa.
Editorial Material
Crystallography
T. Doohun Kim, Kyeong Kyu Kim
Article
Chemistry, Multidisciplinary
Sungwoo Lee, Insub Jung, Soohyun Lee, Eunbyeol Cho, Sangbaek Jung, Seongkeun Ih, Yang-Gyun Kim, Seunghun Hong, Yoon-La Choi, Junghyun Shin, Sungho Park
Summary: We present active plasmonic systems that modulate plasmonic signals by changing the orientation of nanoprobes under an external magnetic field, enabling in situ nanorheology measurements of intracellular viscosity. Au/Ni/Au nanorods transmit mechanical motion to an electromagnetic radiation signal via a periodic sine function. This fluctuating optical response is transformed to frequency peaks by Fourier transform surface plasmon resonance (FTSPR). By increasing the driving frequency of the magnetic field, the synchronous motion of nanorods transitions to asynchronous responses, resulting in the disappearance of the FTSPR peak, allowing for measurement of local viscosity of complex fluids.
Article
Multidisciplinary Sciences
Hackwon Do, Wanki Yoo, Ying Wang, Yewon Nam, Seung Chul Shin, Han-Woo Kim, Kyeong Kyu Kim, Jun Hyuck Lee
Summary: In this study, a novel microbial acetylesterase, LgEstI, was characterized and found to prefer short acyl chains and exhibit increased activity with F207A mutation. Comparative analysis revealed that LgEstI has a narrow and shallow active site, potentially exhibiting substrate specificity to short acyl chains. Immobilized LgEstI retained approximately 90% of its initial activity, suggesting its potential in industrial applications.
Correction
Food Science & Technology
Yang Gyun Kim, Sang Ho Lee, Su Woong Jung, Gun Tae Jung, Hyun Ji Lim, Kwang Pyo Kim, Young-Il Jo, KyuBok Jin, Ju Young Moon
Article
Geriatrics & Gerontology
Wonsuk Oh, Minhae Cho, Su Woong Jung, Ju-Young Moon, Sang-Ho Lee, You-Cheol Hwang, Yang Gyun Kim
Summary: This study found that low physical activity (PA) and prolonged sedentary time (ST) increase the risk of developing chronic kidney disease (CKD) in middle-aged Koreans.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Health Care Sciences & Services
Jihyun Baek, Hyeyeon Lee, Taeyoung Yang, So-Young Lee, Yang Gyun Kim, Jin Sug Kim, ShinYoung Ahn, Kipyo Kim, Seok Hui Kang, Min-Jeong Lee, Dong-Young Lee, Hye Yun Jeong, Yu Ho Lee
Summary: In this study, researchers aimed to identify circulating inflammatory biomarkers that could predict future arteriovenous fistula dysfunction in hemodialysis patients. They found that plasma interleukin-6 (IL-6) levels were positively associated with the occurrence of AVF dysfunction.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Sun-Il Yun, Chulhwan Kwak, Song-Yi Lee, Sanghee Shin, Changsuk Oh, Jong-Seo Kim, Hyun-Woo Rhee, Kyeong Kyu Kim
Summary: This study reveals that ubiquitin-specific protease 4 (USP4) is highly expressed in colon cancer and acts as a potent protooncogenic protein by deubiquitinating beta-catenin. In addition to its well-known role, it is also found that USP4 interacts with cortactin (CTTN) to promote cell dynamics and migration. The dual role of USP4 in cancer progression, involving the stabilization of beta-catenin and the interaction with CTTN, suggests that USP4 is an important target for cancer treatment or prevention.
Article
Chemistry, Multidisciplinary
Jinyoung Byun, Srivithya Vellampatti, Prathit Chatterjee, Sun Ha Hwang, Byoung Choul Kim, Juyong Lee
Summary: A significant difference between APP695 and APP751 isoforms is the presence of the Kunitz type protease inhibitor (KPI) domain, which affects the dimerization of APP isoforms. Through experiments and simulations, it was discovered that homo-dimerization is favored for both isoforms, while hetero-dimerization is limited between APP751 and APP695. The KPI domain has a stronger attractive interaction with itself and other domains in APP751, leading to its predominant homo-dimer formation.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Dae Kyu Kim, Seok Hui Kang, Jin Sug Kim, Yang Gyun Kim, Yu Ho Lee, Dong-Young Lee, Shin Young Ahn, Ju Young Moon, Sang Ho Lee, Kyung Hwan Jeong, Hyeon Seok Hwang
Summary: FSTL-1 is a secreted glycoprotein that regulates cardiovascular, immune, and skeletal systems. In hemodialysis patients, high circulating FSTL-1 levels independently predict the risk of cardiovascular events and death, and are associated with left ventricular systolic dysfunction.
SCIENTIFIC REPORTS
(2023)
Article
Immunology
Jung-Woo Seo, Yu Ho Lee, Dong Hyun Tae, Yang Gyun Kim, Ju-Young Moon, Su Woong Jung, Jin Sug Kim, Hyeon Seok Hwang, Kyung-Hwan Jeong, Hye Yun Jeong, So-Young Lee, Byung Ha Chung, Chan-Duck Kim, Jae Berm Park, Junhee Seok, Yeong Hoon Kim, Sang-Ho Lee
Summary: This study aimed to identify novel biomarkers for the diagnosis of acute rejection (AR) in kidney transplant recipients by examining urinary exosomal microRNAs. Candidate microRNAs were selected through urinary exosomal microRNA profiling, meta-analysis, and literature review. A three-microRNA AR signature, consisting of hsa-miR-21-5p, hsa-miR-31-5p, and hsa-miR-4532, showed promising diagnostic power in discriminating recipients with AR from those with stable graft function.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Do-Yun Lee, Jun-Yeong Jeong, Seung-Eun Lee, Jae-Hun Lee, Ju-Young Moon, Su Woong Jung, Sang-Ho Lee, Yang Gyun Kim
Summary: This case report presents a pair of male monozygotic twins with Fabry disease (FD) who exhibit different renal phenotypes. Genetic testing revealed identical mutations in the twins, as well as in their mother, older sister, and daughter. The findings suggest that environmental or epigenetic factors may play a critical role in genotype-phenotype discordance.
FRONTIERS IN GENETICS
(2023)
Meeting Abstract
Transplantation
Yang-Gyun Kim, Sang-Ho Lee, Ju-Young Moon, Su Woong Jung, Jihoon Park, In Tae Jin, Yoosun Joo, Minhae Cho
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2023)
Meeting Abstract
Transplantation
Yang-Gyun Kim, Sang-Ho Lee, Ju-Young Moon, Su Woong Jung, Kyung Hwan Jeong, Hyeon Seok Hwang, Jin Sug Kim, Minhae Cho
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2023)
Review
Chemistry, Physical
Xuelin Jin, Shrute Kannappan, Natalia Diyah Hapsari, Yu Jin, Kyeong Kyu Kim, Jung Heon Lee, Kyubong Jo
Summary: Electron microscopy-based DNA imaging is a powerful tool for observing genomic structures involved in biochemical processes. Existing methods such as heavy metal shadow casting and uranyl acetate staining have limitations due to government regulations and complicated sample preparation. Nanoparticles and nanowires have emerged as promising alternatives, but further development is needed.
Article
Cell & Tissue Engineering
Gary Stanley Fernandes, Rishabh Deo Singh, Debojyoti De, Kyeong Kyu Kim
Summary: A new chemical-based method for directly converting human fibroblasts into mature neuron-like cells with a short duration and high conversion efficiency is developed in this study. It is also found that extended epigenetic regulation is necessary to maintain neuronal programming and generate a homogeneous population of neuron-like cells.
INTERNATIONAL JOURNAL OF STEM CELLS
(2023)