Article
Plant Sciences
Yujun Ren, Mengsi Li, Wanzhen Wang, Wei Lan, Dirk Schenke, Daguang Cai, Ying Miao
Summary: This study demonstrates that MIR840 negatively regulates gene expression by promoting target mRNA cleavage and impairing translation, particularly affecting plant senescence through the targeting of PPR and WHY3 genes. Knockdown of both PPR and WHY3 in wild-type plants resulted in a senescence phenotype resembling that of the MIR840-overexpressing plant, indicating their crucial role in the MIR840-mediated senescence pathway.
Review
Biochemistry & Molecular Biology
Pilar Menendez-Gil, Alejandro Toledo-Arana
Summary: Bacterial 3' UTRs have emerged as important regulators in processes such as virulence, iron metabolism, and biofilm formation, through mechanisms such as interaction with the 5' UTR of the same transcript, specific targeting by ribonucleases, RNA-binding proteins, and sRNAs, and acting as reservoirs of trans-acting sRNAs. Recent findings also discuss the differential evolution of bacterial 3' UTRs and its impact on species-specific gene expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ida Manna, Francesco Fortunato, Selene De Benedittis, Ilaria Sammarra, Gloria Bertoli, Angelo Labate, Antonio Gambardella
Summary: Temporal lobe epilepsy is the most common form of focal epilepsy, considered a network disorder associated with structural changes. Non-coding RNAs, acting as epigenetic factors, participate in the regulation of the pathophysiological processes of epilepsy and can be used as biomarkers for diagnosis and treatment response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Pharmacology & Pharmacy
Juhee Ryu, Youngkeun Ahn, Hyun Kook, Young-Kook Kim
Summary: This article reviews the role and therapeutic implications of non-coding RNAs (ncRNAs) in vascular calcification (VC). Studies suggest that ncRNAs, including miRNAs, lncRNAs, and circRNAs, play important roles in regulating VC and may be useful in clinical diagnosis and treatment.
PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Biochemistry & Molecular Biology
Dylan J. Kiltschewskij, Paul F. Harrison, Chantel Fitzsimmons, Traude H. Beilharz, Murray J. Cairns
Summary: Differentiation of neural progenitor cells into mature neuronal phenotypes relies on extensive temporospatial coordination of mRNA expression. Cleavage and polyadenylation of mRNA has regulatory capacity through the alteration of mRNA stability and modulation of miRNA function. Our findings suggest poly(A) tail length and APA function as part of a rich post-transcriptional regulatory matrix during neuronal differentiation.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Pathology
Bayu Indra Sukmana, Sulieman Ibraheem Shelash Al-Hawary, Munther Abosaooda, Mohaned Adile, Reena Gupta, Ebraheem Abdu Musad Saleh, Enas R. Alwaily, Hashem O. Alsaab, I. B. Sapaev, Yasser Fakri Mustafa
Summary: miRNA-214 plays a significant role in tumor development by controlling various biological processes. It is located in the q24.3 arm of the human genome and is involved in inducing apoptosis in cancer cells.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Review
Clinical Neurology
Xiao Ling, Jun Lu, Jun Yang, Hanjun Qin, Xingqi Zhao, Pengyu Zhou, Shaoyi Zheng, Peng Zhu
Summary: This study aims to explore the role of non-coding RNAs in attenuating spinal cord ischemia-reperfusion injury (SCIRI) and summarize the current research on the function of ncRNAs in SCIRI, providing new insights for identifying novel therapeutic targets.
FRONTIERS IN NEUROLOGY
(2021)
Article
Immunology
Xuezhi Zhou, Rong Rong, Siqi Xiong, Weitao Song, Dan Ji, Xiaobo Xia
Summary: In this study, a ceRNA regulatory network related to SKCM was identified and potential diagnostic and prognostic markers were identified. Two ceRNA axes were established as prognostic models, providing a novel and important approach for the diagnosis and prognosis of SKCM.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Oncology
Sepideh Mirzaei, Mahshid Deldar Abad Paskeh, Elena Okina, Mohammad Hossein Gholami, Kiavash Hushmandi, Mehrdad Hashemi, Azuma Kalu, Ali Zarrabi, Noushin Nabavi, Navid Rabiee, Esmaeel Sharifi, Hassan Karimi-Maleh, Milad Ashrafizadeh, Alan Prem Kumar, Yuzhuo Wang
Summary: This review highlights the role of epigenetic alterations in the development of prostate cancer, specifically focusing on lncRNAs. Aberrant expression of lncRNAs in prostate cancer is well-documented, affecting various molecular pathways and regulating tumor progression. Additionally, lncRNAs play a role in radio-resistance, chemo-resistance, and immune evasion of prostate cancer, making them potential targets for therapeutic interventions.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Virology
Devin N. Fachko, Yan Chen, Rebecca L. Skalsky
Summary: It has been found that EBV miR-BHRF1-3 can suppress lytic replication by directly inhibiting Zta expression. Moreover, nucleotide variants that impact the function of miR-BHRF1-3 have been identified, which may contribute to specific EBV pathologies.
JOURNAL OF VIROLOGY
(2022)
Article
Geochemistry & Geophysics
Afei Liu, Shuanghui Zhang, Chi Zhang, Shuaifeng Zhi, Xiang Li
Summary: This article introduces a novel 3-D reconstruction method, called radar neural radiance fields (RaNeRF), which can directly reconstruct the 3-D structure of targets using only observed ISAR image sequences without explicit feature extraction and correlation. The proposed method represents the 3-D structure of a target as a continuous 6-D function of space positions and viewing directions using a fully connected deep network, and establishes the relationship between the 3-D structure and 2-D ISAR images for differential rendering. The results demonstrate the effectiveness of the proposed method in reconstructing the 3-D structure of targets and generating more complete and accurate ISAR images.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2023)
Article
Biochemistry & Molecular Biology
Chun-Jie Liu, Xin Fu, Mengxuan Xia, Qiong Zhang, Zhifeng Gu, An-Yuan Guo
Summary: SNVs in miRNAs can impact miRNA functions and biogenesis, affecting phenotypes. miRNASNP-v3 is a database with a vast number of SNVs and new features, offering various functions for research on miRNA-related variations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Yang Liu, Xingshu Zhang, Xuechao Cheng, Qian Luo, Mingyang Yu, Kaijun Long, Wendong Qu, Yang Tang, Ming Gong, Lubiao Liang, Xixian Ke, Yongxiang Song
Summary: This study identified 12 fatty acid metabolism-related long non-coding RNAs that are highly associated with the progression of lung adenocarcinoma (LUAD) and constructed a risk score model for clinical reference. It aims to shed light on the immunology and molecular mechanisms of LUAD and provide hope for its treatment.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Tae-Jun Kim, Yu Gyung Kim, Won Jung, Sungil Jang, Hyoung-Gon Ko, Chan Ho Park, Jin-Seok Byun, Do-Yeon Kim
Summary: Oral lichen planus (OLP) is a chronic inflammatory disease caused by various factors. Non-coding RNAs play a critical role in OLP pathogenesis.
Article
Medicine, General & Internal
Rujuan Wang, Sha Xue, Yaquan Liu, Mi Peng, Bei Guo
Summary: The study revealed a close correlation of lncRNA NEAT1 and its targets miR-21 and miR-125a with disease risk, severity, and inflammation of allergic rhinitis, suggesting their potential as biomarkers for AR assessment.
Article
Chemistry, Physical
Julien Roulet, Seonghoon Choi, Jiri Vanicek
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Tomislav Begusic, Jiri Vanicek
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Physics, Multidisciplinary
Nikolay Golubev, Tomislav Begusic, Jiri Vanicek
PHYSICAL REVIEW LETTERS
(2020)
Article
Chemistry, Physical
Seonghoon Choi, Jiri Vanicek
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Multidisciplinary
Tomislav Begusic, Jiri Vanicek
Summary: Understanding light-induced processes in biological and human-made molecular systems is a main goal of physical chemistry. Theoretical simulation is needed to understand how dynamics translates into spectral features. Recent developments in computation of vibrationally resolved electronic spectra are reviewed, presenting a theoretical approach for computing such spectra beyond commonly used approximations. The combined method can treat all three effects and is applied to compute the absorption spectra of azulene.
Article
Chemistry, Physical
Julien Roulet, Jiri Vanicek
Summary: The explicit split-operator algorithm is not suitable for all types of nonlinear Schrodinger equations, leading to the proposal of high-order geometric integrators suitable for general time-dependent nonlinear Schrodinger equations. These integrators, based on the symmetric compositions of the implicit midpoint method, are both norm-conserving and time-reversible, showing good performance in numerical experiments.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Seonghoon Choi, Jiri Vanicek
Summary: The study introduces a method to assess the potential errors introduced by neglecting residual couplings by comparing quantum dynamics simulations with or without these couplings. The results show that neglecting residual couplings can lead to inaccurate dynamics, while simulations with the exact quasidiabatic Hamiltonian always yield accurate results.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Tomislav Begusic, Jiri Vanicek
Summary: An exact finite-temperature expression for vibrational dynamics is derived using the concept of thermo-field dynamics, allowing for an intuitive wavepacket-based interpretation. The new method combines this exact approach with the thawed Gaussian approximation to compute finite-temperature two-dimensional spectra efficiently, providing insight into symmetry breaking and deviation from traditional models in the signal.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Seonghoon Choi, Jiri Vanicek
Summary: Ehrenfest dynamics is a useful approximation for treating electronically nonadiabatic effects in mixed quantum-classical molecular dynamics, which conserves the total molecular energy and the norm of the electronic wavefunction. Efficient geometric integrators have been developed for representation-free Ehrenfest dynamics, ensuring accuracy regardless of the time step used.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Physics, Multidisciplinary
Nikolay Golubev, Jiri Vanicek, Alexander Kuleff
Summary: This study reports an extension of the theory underlying attosecond transient absorption spectroscopy for molecules, successfully demonstrated on tracking the electron dynamics oscillations in propiolic acid molecule, and shows that the resolution of ATAS enables tracing electron density dynamics with atomic spatial resolution.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Alan Scheidegger, Jiri Vanicek, Nikolay V. Golubev
Summary: By using advanced computational methods and efficient nuclear dynamics evaluation, we conducted a comprehensive study on small polyatomic molecules with long-lasting oscillatory dynamics of electron density triggered by outer-valence ionization. We found that in most molecules, the sudden removal of an electron either does not lead to the appearance of electronic coherence or the created coherences are quickly damped by nuclear rearrangement within a few femtoseconds. However, we identified several unexplored molecules with electron coherences lasting up to 10 fs, which can be promising candidates for experimental studies. Furthermore, we performed full-dimensional simulations of electron coherences coupled with nuclear motion in several molecules that were previously only studied under the fixed nuclei approximation.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Julien Roulet, Jiri Vanicek
Summary: The paper introduces a family of high-order implicit split-operator algorithms to solve nonlinear time-dependent Schrodinger equations, overcoming the limitations of explicit split-operator algorithms. These algorithms are norm-conserving, time-reversible, and efficient, applicable to local control of a two-dimensional retinal model.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Tomislav Begusic, Enrico Tapavicza, Jiri Vanicek
Summary: This study explores the applicability of the single-Hessian thawed Gaussian approximation for simulating the vibrational resolved electronic spectra of anharmonic systems. The method is shown to be more robust and accurate than the traditional harmonic approximation, especially in cases where the harmonic approximation breaks down.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Nikolay V. Golubev, Jiri Vanicek
Summary: In this article, we review a newly developed theoretical approach for evaluating electronic coherences in polyatomic molecules. This technique combines ultrafast electronic dynamics with nuclear motion and utilizes ab initio calculations for electronic structure and semiclassical procedures for nuclear wave packet dynamics. It provides high computational efficiency and helps to uncover the physical mechanisms of electronic coherence decay and revival driven by nuclear rearrangement.
Article
Chemistry, Physical
Tomislav Begusic, Jiri Vanicek
JOURNAL OF CHEMICAL PHYSICS
(2020)
