Article
Chemistry, Physical
Flore Mekki-Berrada, Zekun Ren, Tan Huang, Wai Kuan Wong, Fang Zheng, Jiaxun Xie, Isaac Parker Siyu Tian, Senthilnath Jayavelu, Zackaria Mahfoud, Daniil Bash, Kedar Hippalgaonkar, Saif Khan, Tonio Buonassisi, Qianxiao Li, Xiaonan Wang
Summary: This study presents a two-step framework for rapidly producing silver nanoparticles with desired absorbance spectrum using a machine learning-driven high-throughput microfluidic platform. By combining Bayesian optimization and deep neural network, the framework efficiently optimizes nanomaterial synthesis and extracts knowledge of the relationship between chemical composition and optical properties.
NPJ COMPUTATIONAL MATERIALS
(2021)
Article
Multidisciplinary Sciences
Huijun Xue, Amit Bhardwaj, Yandong Yin, Carel Fijen, Anastasiya Ephstein, Lianglin Zhang, Xia Ding, John M. Pascal, Todd L. VanArsdale, Eli Rothenberg
Summary: PARP inhibitors modulate the retention of PARP1 on DNA lesions through a two-step mechanism, involving competitive inhibition of NAD(+) binding and allosteric modulation. The retention potency of PARPi is predominantly determined by its ability to outcompete NAD(+) binding.
Article
Environmental Sciences
Jia-Yue Wang, Jing-Xin Li, Jing Ning, Xiao-Kui Huo, Zhen-Long Yu, Yan Tian, Bao-Jing Zhang, Yan Wang, Deng Sa, Ya-Chen Li, Xia Lv, Xiao-Chi Ma
Summary: This study investigates the oxidative metabolism of Dimethomorph (DMM) mediated by the human cytochrome P450 enzyme (CYP) and its toxicological effects. The study reveals that DMM is mainly metabolized through a two-step oxidation process mediated by CYP3A, and can cause mechanism-based inactivation (MBI) of CYP3A. Additionally, other common fungicides can inhibit the metabolism of DMM, leading to increased exposure to DMM in vivo.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Multidisciplinary
Vimukthi Pathirage, Salma Khatun, Sergey Lisenkov, Kinga Lasek, Jingfeng Li, Sadhu Kolekar, Manuel Valvidares, Pierluigi Gargiani, Yan Xin, Inna Ponomareva, Matthias Batzill
Summary: Inserting metal layers between layered transition-metal dichalcogenides (TMDs) enables the design of new nano materials. By inserting Cr or Mn between VSe2 layers, controlled synthesis of nano materials can be achieved, and the interactions between transition metals and TMDs can be studied.
Article
Materials Science, Multidisciplinary
Provakar Paul, Monaj Karar, Arabinda Mallick, Tapas Majumdar
Summary: This multifunctional molecular logic system utilizes the differential fluorescence readouts at three wavelengths to perform a variety of logic functions, including single-input-single-output and dual-input-single-output logic gates, as well as combinational logic gates and logically reversible gates. The logic outcome can be effortlessly switched by changing chemical inputs and optical outputs, providing a new approach for fabricating molecular integrated circuits (MICs).
JOURNAL OF MATERIALS CHEMISTRY C
(2021)
Article
Optics
Vincent Hahn, Pascal Rietz, Frank Hermann, Patrick Mueller, Christopher Barner-Kowollik, Tobias Schloeder, Wolfgang Wenzel, Eva Blasco, Martin Wegener
Summary: In recent years, there has been a growing interest in high-speed, high-resolution optics-based 3D printing technology. By combining image projection with optical nonlinearity, researchers have successfully achieved high printing rates with small voxel volumes.
Article
Biochemistry & Molecular Biology
Fayezeh Samari, Bahram Hemmateenejad, Santiago Aparicio, Mehdi Rashidi, Mojtaba Shamsipur, Sayed Mostafa Hosseini
Summary: The binding interaction between two organoplatinum complexes and calf thymus DNA (CT-DNA) was investigated using various biophysical techniques. The results showed that the complexes exhibited a tight intercalative interaction with CT-DNA, which was confirmed by both experimental and computational studies. These findings suggest that these organoplatinum complexes have potential for cancer therapeutic applications.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Kristie D. Goodwin, Mark A. Lewis, Eric C. Long, Millie M. Georgiadis
Summary: Bleomycins are anticancer natural products that bind DNA through intercalation and hydrogen-bonding interactions. The C-terminal tail was found to play a role in directing the intercalation of the bithiazole. Specific bond rotations within the C-terminal domain of the drug were identified and may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Suk Woo Lee, Lu Qiu, Jong Chan Yoon, Yohan Kim, Da Li, Inseon Oh, Gil-Ho Lee, Jung-Woo Yoo, Hyung-Joon Shin, Feng Ding, Zonghoon Lee
Summary: The intercalation of copper in black phosphorus leads to anisotropic changes in electronic channels, transitioning from semiconductor to semimetal. The research also reveals the intercalation mechanism where copper atoms are inserted from top down, shedding light on the fundamental relationship between microstructure changes and properties in intercalated black phosphorus. The study demonstrates the potential for tailoring anisotropic 2D materials at the angstrom scale.
Article
Engineering, Environmental
Emmanouil Androulakis, George Galanis
Summary: The study proposes a two-step hybrid system combining the WAM model and gradient boosting regression tree algorithm to optimize wave height forecasts, using only information from the WAM model as features. The predictive performance of the system is evaluated in three study areas, demonstrating its increased accuracy compared to the original WAM model and significant reduction in systematic error.
STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT
(2022)
Article
Engineering, Chemical
Wenyu Zhong, Dongdong Hu, Yichong Chen, Ling Zhao
Summary: The batch foaming of supercritical fluids faces challenges in controllability and productivity due to temperature changes and non-uniformity during foaming. To overcome these challenges, a unique two-step foaming method combined with microwave enhancement was proposed. This method resulted in higher expansion ratio foams with lower density and more uniform cells compared to existing methods. Additionally, a conduction-microwave (C-M) heating mechanism was innovatively introduced to improve heating efficiency and uniformity.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Polymer Science
Jesse Kuebler, Tucker Loosbrock, Joseph Strzalka, Lucia Fernandez-Ballester
Summary: A two-step stratified crystallization process was observed during the cooling of poly(3-hexylthiophene) (P3HT) thin films. The crystallization temperature of a thin surface layer was found to be higher than that of the bulk of the film, indicating a surface-induced process. In contrast, the underlayer of the film crystallized at a temperature near the bulk crystallization temperature.
Article
Biology
Jixue Sun, Fei Liu, Longxiao Yuan, Ning-Ning Pang, Bing Zhu, Na Yang
Summary: This study elucidates the activation mechanism of DNMT1 using various sampling methods. The results show that the binding of H3Ub2 to the RFTS domain of DNMT1 leads to conformational changes, activating DNMT1.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Chemistry, Physical
Miriama Simunkova, Monika Biela, Marek Steklac, Andrej Hlinc, Erik Klein, Michal Malcek
Summary: This study investigates the antioxidant and DNA-intercalating properties of Cu(II)-flavonoid complexes. The results demonstrate enhanced radical scavenging activity and improved DNA intercalating ability in flavonoid complexes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Spectroscopy
Jolanta Sochacka, Marcin Pacholczyk, Malgorzata Jelen, Beata Morak-Mlodawska, Krystian Pluta
Summary: In this study, the interaction mode of selected azaphenothiazines (AZA) with calf thymus DNA was investigated using UV-Vis absorption, fluorescence spectroscopy, and molecular docking. The results showed that AZA bind to DNA by inserting a fragment of the fused rings system between the base pair stack in the double helix. The number of rings in the AZA structures seemed to be correlated with the strength of the interaction, with pentacyclic AZA demonstrating higher affinity towards DNA.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Biochemistry & Molecular Biology
Vandana Singh, Pegah Johansson, Elina Ekedahl, Yii-Lih Lin, Ola Hammarsten, Fredrik Westerlund
Summary: In this study, single DNA molecule imaging using fluorescence microscopy was used to quantify DNA damage caused by the topoisomerase II poison etoposide. The researchers found a large variation in etoposide-induced DNA damage after in vitro treatment of blood cells from healthy individuals. The results further demonstrated that the etoposide-induced DNA damage was TopoII dependent.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Infectious Diseases
K. K. Sriram, Elina Ekedahl, Ngoc Thi Bich Hoang, Tsegaye Sewunet, Bjorn Berglund, Ludwig Lundberg, Shoeib Nematzadeh, Maud Nilsson, Lennart E. Nilsson, Ngai Kien Le, Dien Minh Tran, Hakan Hanberger, Linus Olson, Mattias Larsson, Christian G. Giske, Fredrik Westerlund
Summary: The diversity of bla(NDM-1)-encoding plasmids from neonates at a large Vietnamese hospital was characterized using optical DNA mapping (ODM) and next-generation sequencing (NGS). The results showed that there were at least 10 different plasmids encoding bla(NDM-1) among the 18 isolates, indicating wide plasmid diversity. This study highlights the importance of ODM for plasmid analysis.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Virology
Helena Gien, Michael Morse, Micah J. McCauley, Jonathan P. Kitzrow, Karin Musier-Forsyth, Robert J. Gorelick, Ioulia Rouzina, Mark C. Williams
Summary: In this study, the researchers used optical tweezers, fluorescence imaging, and atomic force microscopy to observe the binding modes of the HIV-1 nucleocapsid protein (NC) to a DNA substrate. They found that NC can bind to and condense the DNA into a tight globule in a non-specific binding mode, and that specifically-bound NC maintains long-range DNA looping. These results provide insights into how NC helps stabilize the viral DNA genome within the viral capsid.
Article
Infectious Diseases
Tsegaye Sewunet, Daniel Asrat, Yimtubezinash Woldeamanuel, Sofia Ny, Fredrik Westerlund, Abraham Aseffa, Christian G. Giske
Summary: This study investigated the genome-based epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia. The study found a high prevalence of ESBL-EC, with dissemination through multiple high-risk E. coli clones.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2022)
Article
Biophysics
Adam A. Jabak, Nicholas Bryden, Fredrik Westerlund, Per Lincoln, Micah J. McCauley, Ioulia Rouzina, Mark C. Williams, Thayaparan Paramanathan
Summary: The study reveals that the left-handed enantiomer requires more DNA lengthening for threading and extends the DNA more than the right-handed enantiomer at equilibrium. Additionally, the left-handed complex unthreads three times faster than the right-handed complex. These results suggest a preference in DNA binding to the chiral enantiomer having the same chirality as the DNA molecule.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemical Research Methods
Barbora Spackova, Henrik Klein Moberg, Joachim Fritzsche, Johan Tenghamn, Gustaf Sjosten, Hana Sipova-Jungova, David Albinsson, Quentin Lubart, Daniel van Leeuwen, Fredrik Westerlund, Daniel Midtvedt, Elin K. Esbjorner, Mikael Kall, Giovanni Volpe, Christoph Langhammer
Summary: Nanofluidic scattering microscopy (NSM) is a label-free, real-time imaging technique that enables measurement of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles inside a nanofluidic channel. It provides a method for characterizing single biomolecules without the need for labeling, which can compromise data interpretation.
Article
Biochemistry & Molecular Biology
Ben A. Cashen, M. Nabuan Naufer, Michael Morse, Charles E. Jones, Mark C. Williams, Anthony Furano
Summary: This article investigates the function and structure of long interspersed nuclear element 1 (L1), and reveals that the coiled coil (CC) domain governs the ability of retrotransposition-competent ORF1p trimers to form tightly compacted complexes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Michael Morse, Jana Sefcikova, Ioulia Rouzina, Penny J. Beuning, Mark C. Williams
Summary: The SARS-CoV-2 nucleocapsid (N) protein plays a crucial role in binding and packaging the viral genome into the viral particle. It consists of two domains, with the N-terminal domain primarily involved in RNA binding and the C-terminal domain primarily involved in dimerization/oligomerization. The study used an optical tweezers system to observe the binding and packaging function of the protein at a single molecule level in real time.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Micah J. McCauley, Michael Morse, Nicole Becker, Qi Hu, Maria Victoria Botuyan, Emily Navarrete, Ran Huo, Uma M. Muthurajan, Ioulia Rouzina, Karolin Luger, Georges Mer, James Maher, Mark C. Williams
Summary: The histone chaperone FACT enhances transcription by targeting DNA-protein interactions. This study demonstrates the impact of FACT on nucleosome stability and dynamics, revealing contradictory functions of different FACT subdomains in nucleosome remodeling. These findings provide insights into the catalytic role of key FACT domains in nucleosome disassembly and reassembly.
Article
Nanoscience & Nanotechnology
John Andersson, Julia Jarlebark, K. K. Sriram, Andreas Schaefer, Rebekah Hailes, Chonnipa Palasingh, Bagus Santoso, Van-Truc Vu, Chun-Jun Huang, Fredrik Westerlund, Andreas Dahlin
Summary: In nanobiotechnology, controlling the interactions between biological molecules and surfaces is crucial. This study presents a simple method for passivating or selectively functionalizing silica surfaces, without the need for complex reactions. The modified surfaces show superior properties compared to existing options, with low fouling and the ability to detect specific molecules. This method is compatible with various surface-based sensors and analytical devices, making it highly valuable for the field of nanobiotechnology.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Bjorn Altenburger, Carl Andersson, Sune Levin, Fredrik Westerlund, Joachim Fritzsche, Christoph Langhammer
Summary: This study introduces nanofluidic scattering microscopy to measure the activity of single nanoparticles during catalytic reactions. By detecting minuscule refractive index changes in the liquid, the concentration changes of reactants can be accurately measured. The turnover frequency of the particles is derived from the growth rate of gas bubbles formed during the reaction.
Article
Medicine, Research & Experimental
My Nyblom, Anna Johnning, Karolin Frykholm, Marie Wrande, Vilhelm Mueller, Gaurav Goyal, Miriam Robertsson, Albertas Dvirnas, Tsegaye Sewunet, K. K. Sriram, Tobias Ambjornsson, Christian G. Giske, Linus Sandegren, Erik Kristiansson, Fredrik Westerlund
Summary: We have developed a method to directly identify bacteria from patient samples, which can accurately identify different strains or subtypes. This method can be used for mixed bacterial samples and urine samples, providing fast diagnostic information for choosing the most suitable antibiotics and reducing the risk of death and suffering.
COMMUNICATIONS MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Nima Sasanian, Rajhans Sharma, Quentin Lubart, K. K. Sriram, Marziyeh Ghaeidamini, Kevin D. Dorfman, Elin K. Esbjorner, Fredrik Westerlund
Summary: Amyloid fibrils play a central role in the pathology of many diseases and have significant structural polymorphism. A nanofluidic channel analysis technique was introduced to study single, fluorescently-labeled amyloid fibrils and determine their physical properties. The method allowed for accurate determination of fibril persistence length and revealed differences in physical properties between amyloid-beta(1-42) and alpha-synuclein fibrils.
Article
Infectious Diseases
Kk Sriram, Moa S. Wranne, Tsegaye Sewunet, Elina Ekedahl, Maarten Coorens, Teerawit Tangkoskul, Visanu Thamlikitkul, Christian G. Giske, Fredrik Westerlund
Summary: This study demonstrates the use of optical DNA mapping (ODM) to characterize plasmids carrying the colistin resistance gene mcr-1. The researchers successfully identified plasmids encoding mcr-1 and demonstrated the ability of ODM to identify resistance gene sites in small plasmids. They also propose a cut-and-stretch assay using surface-functionalized cover slips and a basic microscope to identify the mcr-1 gene in plasmid samples. These techniques could be valuable in identifying plasmids carrying antibiotic resistance in hospitals, particularly in low- and middle-income countries.
JAC-ANTIMICROBIAL RESISTANCE
(2022)
Meeting Abstract
Biophysics
Fredrik Westerlund
BIOPHYSICAL JOURNAL
(2022)
