Article
Genetics & Heredity
Mariana Saint Just Ribeiro, Pulak Tripathi, Bahram Namjou, John B. Harley, Iouri Chepelev
Summary: This study elucidates the haplotype-specific mechanisms of gene regulation at 8p23.1 in the human genome and reveals how distal regulatory elements modulate promoter activity, influencing disease risk by changing gene expression. The results provide mechanistic details on how regional variants controlling gene promoters may impact disease risk.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Multidisciplinary
Maria E. F. Brollo, Ivanei F. Pinheiro, Gabriel S. Bassani, Guillaume Varet, Daniel Merino-Garcia, Vanessa C. B. Guersoni, Marcelo Knobel, Antonio C. Bannwart, Charlie van der Geest, Diego Muraca
Summary: Flow assurance is crucial for successful crude oil extraction, as it ensures a financially sustainable flow and addresses issues such as paraffin deposition, asphaltene, and methane hydrate. The application of magnetic nanoparticles in the oil industry is a recent research focus, where the use of magnetic nanofluids and the phenomenon of magnetic hyperthermia can significantly decrease viscosity.
Article
Chemistry, Multidisciplinary
Maria E. F. Brollo, Ivanei F. Pinheiro, Gabriel S. Bassani, Guillaume Varet, Daniel Merino-Garcia, Vanessa C. B. Guersoni, Marcelo Knobel, Antonio C. Bannwart, Charlie van der Geest, Diego Muraca
Summary: Flow assurance is crucial for crude oil extraction, and heating the fluids using magnetic nanoparticles can effectively reduce viscosity and improve oil flow. This study focuses on the use of magnetic NPs in heavy crude oil, and experimentally demonstrates a significant decrease in viscosity and increase in oil production by using magnetic hyperthermia.
Article
Physics, Applied
Samuel D. Sloetjes, Bjoergvin Hjorvarsson, Vassilios Kapaklis
Summary: The magnetization dynamics of nanomagnets excited by stochastic magnetic fields to mimic temperature in a micromagnetic framework were studied, with a focus on the spatial extension of internal magnon modes and the temperature dependence of the modes. Fluctuations in the low frequency edge modes were observed, associated with switching between C- and S-states, creating an energy barrier, which was classified into three different regimes and calculated using the Arrhenius law.
APPLIED PHYSICS LETTERS
(2021)
Article
Oncology
Cristina Montero-Conde, Luis Javier Leandro-Garcia, Angel M. Martinez-Montes, Paula Martinez, Francisco J. Moya, Rocio Leton, Eduardo Gil, Natalia Martinez-Puente, Sonsoles Guadalix, Maria Curras-Freixes, Laura Garcia-Tobar, Carles Zafon, Mireia Jorda, Garcilaso Riesco-Eizaguirre, Patricia Gonzalez-Garcia, Maria Monteagudo, Rafael Torres-Perez, Veronika Mancikova, Sergio Ruiz-Llorente, Manuel Perez-Martinez, Guillermo Pita, Juan Carlos Galofre, Anna Gonzalez-Neira, Alberto Cascon, Cristina Rodriguez-Antona, Diego Megias, Maria A. Blasco, Eduardo Caleiras, Sandra Rodriguez-Perales, Mercedes Robledo
Summary: Comprehensive molecular studies were conducted on thyroid tumors to identify prognostic biomarkers. Telomere-related alterations, especially TERT and TERC, were found in aggressive tumors. Short telomeres led to reorganization in the 5p subtelomeric region, resulting in increased gene upregulation and a more relaxed chromatin configuration in the tumors.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Chuan Shen, Xia Li
Summary: In this study, the characteristics and functions of the P450 gene family in Camellia sinensis were analyzed using bioinformatics-based methods. A total of 273 putative P450 genes were identified, and they were well-balanced across the genome. Phylogenetic analysis divided the CsP450s into 34 subfamilies, with CYP71 being the most abundant. Subcellular localization analysis showed that P450 was distributed in various organelles. The promoter region of CsP450s contained cis-acting elements related to phytohormones and stress responses. Tissue expression analysis revealed that P450 was highly expressed in roots and stems. Furthermore, qPCR analysis confirmed the expression patterns under drought and cold stress.
Article
Food Science & Technology
Chengcong Yang, Lijun You, Lai-Yu Kwok, Hao Jin, Jiangying Peng, Zhixin Zhao, Zhihong Sun
Summary: This study analyzed the microbiomes and metabolomes of Chinese and European cheeses, revealing significant variations between samples from different regions. New species identified through deep metagenome sequencing were found to play a role in cheese flavor formation, while the main differential metabolites between Chinese and European cheeses were amino acids and volatile substances. Additionally, correlations were found between specific cheese-associated bacterial taxa and metabolites, indicating their collective influence on cheese flavor.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Alisa Gega, Athar Ansari
Summary: Introns play a conserved role in enhancing gene expression, with proximity to both the promoter and the terminator regions affecting their regulatory potential. While a promoter-proximal intron is most efficient in enhancing gene expression, a terminator-proximal intron can also positively influence transcription by affecting both the assembly of preinitiation complex and promoter directionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zhongqi Chen, Shawn R. Narum
Summary: The study used low coverage whole-genome resequencing to identify genome regions involved in thermal adaptation in wild redband trout. Selective sweeps among populations and association tests for specific phenotypes under thermal stress were conducted, with a particular focus on the cerk gene on chromosome 4 as a potential candidate gene for local thermal adaptation. Further validation is needed to determine the functional role of cerk in influencing thermal performance.
Article
Biochemistry & Molecular Biology
Henry E. Miller, Daniel Montemayor, Jebriel Abdul, Anna Vines, Simon A. Levy, Stella R. Hartono, Kumar Sharma, Bess Frost, Frederic Chedin, Alexander J. R. Bishop
Summary: R-loops are nucleic acid structures formed from the hybridization of RNA and DNA. This study reprocessed a large number of R-loop mapping datasets and developed an accurate quality control method. The study also revealed differences in R-loop characteristics between different mapping methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Physics, Applied
David Slay, Dongmei Cao, Eric C. Ferre, Michalis Charilaou
Summary: This study reveals that dipole-dipole interactions have a strong effect on the collective magnetic state, despite thermal fluctuations, and should be considered in high-frequency applications. The configuration of iron-oxide nanoparticles has a significant impact on their effective magnetic anisotropy at short time scales, an order of magnitude larger than the intrinsic magnetocrystalline anisotropy.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Cell Biology
Long Vo Ngoc, Torrey E. Rhyne, James T. Kadonaga
Summary: In this study, machine learning was used to compare DPR region, a DNA motif involved in transcription initiation, in humans and Drosophila. A distinct human-specific version of DPR was identified and machine learning models were used to predict synthetic DPR motifs with specificity for human transcription factors. These findings demonstrate the potential of machine learning in designing synthetic DNA elements with specific functional properties.
GENES & DEVELOPMENT
(2023)
Article
Biology
Aaron M. Fleming, Cynthia J. Burrows
Summary: The article discusses the oxidation of guanine in DNA caused by ionizing radiation or the Fenton reaction, focusing on the formation of various oxidized lesions including 8-oxo-7,8-dihydroguanine (OG) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). It compares the pathways and biological consequences of guanine oxidation induced by hydroxyl radicals with endogenous oxidative stress, emphasizing the potential impact on mutagenesis and epigenetics.
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2022)
Article
Immunology
Michael Beckstette, Chia-Wen Lu, Susanne Herppich, Elia C. Diem, Anna Ntalli, Aaron Ochel, Friederike Kruse, Beate Pietzsch, Katrin Neumann, Jochen Huehn, Stefan Floess, Matthias Lochner
Summary: This study identified differentially methylated regions (DMRs) and epigenetic marker regions in murine lymph node-derived ILCs using genome-wide DNA methylation profiling. The marker regions showed strong correlation with the expression of associated genes, suggesting their functional relevance. These epigenetic markers can serve as a tool to study phenotypic and functional properties of ILCs.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biodiversity Conservation
David Renault, Camille Leclerc, Marc-Antoine Colleu, Aude Boutet, Hoel Hotte, Herve Colinet, Steven L. Chown, Peter Convey
Summary: Polar and alpine regions are experiencing rapid changes due to global climate change, affecting biodiversity, particularly invertebrate ectotherms. Short-term extreme temperature events have significant impacts on high-latitude ectotherms, with native species being less resilient than their alien counterparts.
GLOBAL CHANGE BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jean Cadet, J. Richard Wagner, Dimitar Angelov
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Manu Shubhdarshan Shukla, Sajad Hussain Syed, Ramachandran Boopathi, Elsa Ben Simon, Sunil Nahata, Lorrie Ramos, Defne Dalkara, Cendrine Moskalenko, Andrew Travers, Dimitar Angelov, Stefan Dimitrov, Ali Hamiche, Jan Bednar
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Ramachandran Boopathi, Radostin Danev, Maryam Khoshouei, Seyit Kale, Sunil Nahata, Lorrie Ramos, Dimitar Angelov, Stefan Dimitrov, Ali Hamiche, Carlo Petosa, Jan Bednar
NUCLEIC ACIDS RESEARCH
(2020)
Review
Biophysics
Michel Peyrard
JOURNAL OF BIOLOGICAL PHYSICS
(2020)
Article
Biochemistry & Molecular Biology
Adrian Gonzalez, Andrew R. Wildes, Estelle Mossou, Viviana Cristiglio, Gael Moiroux, Jean-Luc Garden, Santiago Cuesta-Lopez, Nikos Theodorakopoulos, Michel Peyrard
Summary: The melting transition of Li-DNA fibers in ethanol-water solutions depends more on the interaction between the DNA and its aqueous environment rather than local confinement. As the ethanol concentration increases, the potentials weaken, DNA becomes less stable, fibers become more compact, and distances between base pairs become more regular.
Article
Biochemistry & Molecular Biology
Dimitar Angelov, Imtiaz Nisar Lone, Herve Menoni, Jean Cadet
Summary: This study demonstrates that ionization of guanine bases in DNA by UVC laser irradiation can induce the formation of interstrand crosslinks. This highlights the diverse reactions of guanine radical cation with various one-electron oxidants and provides examples of relevant biochemical/structural applications.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2022)
Editorial Material
Biology
Jean Cadet, Dimitar Angelov, J. Richard Wagner
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Dimitar Angelov, Ramachandran Boopathi, Imtiaz Nisar Lone, Herve Menoni, Stefan Dimitrov, Jean Cadet
Summary: Interactions between DNA and structural proteins are crucial for cellular processes. The most commonly used method for mapping these interactions is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). However, traditional cross-linking methods have limitations in efficiency, and a new innovative technique using a short UV laser pulse has been introduced to overcome these limitations.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jaime Alegrio Louro, Ramachandran Boopathi, Brice Beinsteiner, Abdul Kareem Mohideen Patel, Tat Cheung Cheng, Dimitar Angelov, Ali Hamiche, Jan Bendar, Seyit Kale, Bruno P. Klaholz, Stefan Dimitrov
Summary: Binding of linker histones generates an asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome structure is unclear. We designed and analyzed a nucleosome with a palindromic DNA sequence to investigate potential asymmetry due to H1. The results showed that H1 restricts linker DNA flexibility and reveals partial asymmetrical unwrapping, but in the palindromic nucleosome, H1 CTD collapses to the proximal linker.
Article
Chemistry, Medicinal
Burcu Ozden, Ramachandran Boopathi, Ayse Bercin Barlas, Imtiaz N. Lone, Jan Bednar, Carlo Petosa, Seyit Kale, Ali Hamiche, Dimitar Angelov, Stefan Dimitrov, Ezgi Karaca
Summary: This work dissects the binding mode of Sox Pioneer Transcription Factors (PTFs) by combining molecular simulations and physiochemistry approaches. The results show that Sox can bind to compact nucleosomes without causing significant conformational changes when the consensus DNA is located on the solvent-facing DNA strand. The study also reveals that both base-specific interactions and Sox-induced DNA changes are required for sequence-specific nucleosomal DNA recognition.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Physics, Fluids & Plasmas
Jean-Luc Garden, Michel Peyrard
Summary: This paper investigates the application of temperature modulated calorimetry in different situations and compares it with standard scanning calorimetry. The study reveals the importance of temperature modulated calorimetry in observing the heat capacity changes in non-equilibrium systems and glassy samples.
Article
Physics, Fluids & Plasmas
Michel Peyrard, Jean-Luc Garden
Article
Engineering, Mechanical
Julien Scheibert, Riad Sahli, Michel Peyrard
FRONTIERS IN MECHANICAL ENGINEERING-SWITZERLAND
(2020)
Proceedings Paper
Materials Science, Multidisciplinary
Maria Luisa Grilli, Daniele Valerini, Radu Robert Piticescu, Tiziano Bellezze, Mehmet Yilmaz, Antonio Rinaldi, Santiago Cuesta-Lopez, Antonella Rizzo
E-MRS FALL SYMPOSIUM I: SOLUTIONS FOR CRITICAL RAW MATERIALS UNDER EXTREME CONDITIONS
(2018)
Review
Engineering, Manufacturing
Marina Urbina, Antonio Rinaldi, Santiago Cuesta-Lopez, Arcadii Sobetkii, Anca Elena Slobozeanu, Peter Szakalos, Yi Qin, Mythili Prakasam, Radu-Robert Piticescu, Cedric Ducros, Alain Largeteau
MANUFACTURING REVIEW
(2018)
