Article
Chemistry, Multidisciplinary
Chengxu Li, Zhigang Li, Wenjie Han, Xue Yin, Xiaoyu Liu, Shiyan Xiao, Haojun Liang
Summary: Modification of the toehold domain or near to it using fluorophore dyes or quenchers can greatly affect the kinetics of the toehold-mediated strand displacement reaction, leading to faster or slower reaction rates.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Yurie Tehee Kim, Hyesoo Oh, Myung Jun Seo, Dong Hyeun Lee, Jieun Shin, Serang Bong, Sujeong Heo, Natalia Diyah Hapsari, Kyubong Jo
Summary: This study constructed 21 FP-DBPs to stain and visualize DNA molecules, with the choice of FP and DBP affecting the brightness and stretching of DNA staining, providing guidance for the development of novel DNA-binding fluorescent proteins.
Article
Chemistry, Organic
Rabi Sankar Das, Ayan Mukherjee, Samiran Kar, Tapas Bera, Shreya Das, Arunima Sengupta, Samit Guha
Summary: This article describes a novel red fluorescent mechanically interlocked molecule with dual targeting functionality for live cancer cell specific active targeting and imaging of malignant lysosomes.
Article
Materials Science, Multidisciplinary
Yike Yang, Yumei Ji, Xu Han, Yunxin Long, Callum Stewart, Yiqiang Wen, Hok Yeung Lee, Tian Cao, Jinsong Han, Sijie Chen, Linxian Li
Summary: The Materials Genome Initiative (MGI) is using high-throughput experimentation, database construction, and intelligence computation to accelerate advanced materials development. In this study, an intelligent combinatorial methodology driven by machine learning is presented for predicting the staining cell ability of dyes. Through high-throughput synthesis and evaluation of 1,536 dyes, a feature dataset for machine learning is established, and high-precision ML-predictors are successfully modeled for live-cell staining and endoplasmic reticulum judgment.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Biochemical Research Methods
Hayley-Ann Bennett, Alyssa McAdorey, Hongbin Yan
Summary: The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.
JOURNAL OF FLUORESCENCE
(2023)
Article
Chemistry, Organic
Wai-Ming Yip, Qiong Yu, Ajcharapan Tantipanjaporn, Wing-Cheung Chan, Jie-Ren Deng, Ben Chi-Bun Ko, Man-Kin Wong
Summary: Quinoliziniums, cationic aromatic heterocycles with a quaternary bridgehead nitrogen, have been synthesized and studied for their photophysical properties. These compounds have shown promising results in visible-light-induced photocatalysis reactions, with good yields up to 65%.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Chemistry, Organic
Hai-Yan Peng, Gang Zhang, Yu-Jie Xu, Ru Sun, Jian-Feng Ge
Summary: In this paper, cationic probes 1a and 1b and a neutral dye 1c were designed and synthesized for the detection of nucleic acids. The probes showed excellent selectivity and an ON-OFF fluorescence response to DNA and RNA with linear correlation between fluorescence intensity and concentration. The probes also demonstrated potential for staining nucleic acids in mitochondria, highlighting their usefulness in low toxicity mitochondrial nucleic acid probes.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Applied
Anastasiya Ershova, Anastasiya U. Alekseeva, Oleg Ershov, Mikhail Yu Ievlev, Ivan N. Bardasov
Summary: The synthesis of novel highly efficient fluorescent dyes was described via heterocyclization of aryl(heteryl)methylidene derivatives of malononitrile dimer bearing electrondonor groups. Solvatochromic behavior and substituents effect on the spectral-luminescent properties were investigated, with strong solvatochromism and high relative fluorescence quantum yields observed despite large Stokes shift values.
Article
Chemistry, Analytical
Anna S. Efimova, Mariya A. Ustimova, Nelly S. Chmelyuk, Maxim A. Abakumov, Yury V. Fedorov, Olga A. Fedorova
Summary: This study synthesized new styryl dyes with N-methylpyridine or N-methylquinoline scaffolds and examined their binding affinity for DNA in cell-free solution. The substitution of heterocyclic residue from pyridine to quinoline and variation in the phenyl part greatly influenced their binding modes, binding affinities, and spectroscopic responses. Biological experiments demonstrated the low toxicity of the synthesized dyes and their ability to selectively stain mitochondria in living cells.
Review
Chemistry, Applied
Qiannan Tang, Hening Li, Haoliang Hu, Linxi Chen
Summary: This review introduces the role of the endoplasmic reticulum (ER) in cellular processes and discusses the research progress of fluorescent probes for imaging physiological or pathological events in the ER. The study contributes to the discovery of targeted therapeutics and promotes interdisciplinary research.
Article
Biotechnology & Applied Microbiology
Kerstin Rastaedter, Andrea Tramontano, David J. Wurm, Oliver Spadiut, Julian Quehenberger
Summary: Currently, the determination of Sulfolobus acidocaldarius cell viability is done through time-lagged plating assays, which are tedious and require a lot of materials. This study explores the use of flow cytometry (FCM) as a faster and more reliable method for viability assessment, using commercially available fluorescent dyes. The developed FCM method was compared to the traditional plating assay in a chemostat cultivation, showing its applicability for bioprocess monitoring.
Article
Environmental Sciences
Jianda Wang, Ying Ma
Summary: This study evaluates the impact of green finance on CO2 emissions using the econometric method and the green finance index. The findings indicate that green finance implementation in China effectively reduces CO2 emissions. However, there are geographical heterogeneity and asymmetry in the relationship between green finance and CO2 emissions. The development of green finance can influence the greenhouse effect by promoting economic growth, constraining energy efficiency improvement, and optimizing industrial structure.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Environmental Sciences
Shikuan Zhao, Yuequn Cao, Chao Feng, Ke Guo, Jinning Zhang
Summary: This study empirically analyzes the effects and mechanisms of environmentally induced R&D and traditional R&D on green total-factor productivity in China. The results indicate that environmentally induced R&D investment significantly promotes the growth of green total-factor productivity, while traditional R&D investment does not have a significant effect. Environmentally induced R&D promotes the growth of green total-factor productivity through channels such as emission reduction, clean energy consumption, and green technology progress.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Jonas Bentz, Ravi A. Patel, Pascal Benard, Alice Lieu, Adrian Haupenthal, Eva Kroener
Summary: Wettability is an important parameter for determining hydrology in porous media, but the influence of spatially heterogeneous wettability distributions is not well understood. This study used numerical simulations to investigate the impact of spatially heterogeneous wettability patterns on infiltration in porous media. The results show that the specific location of wettability patterns within the pore space determines hydraulic dynamics and water repellency.
Article
Chemistry, Physical
Muhammad Salman, Abdul Jabbar, Salma Farooq, Idrees Bashir, Muhammad Sohail Khan Rafiq
Summary: In this research, novel heterocyclic disperse dyes were synthesized using 8-aminonaphthalen-2-ol and different heterocyclic aromatic amines as the coupling and diazonium components, respectively. Various analytical techniques were employed to determine the structure of the synthesized dyes. The solvatochromism and fluorescence properties of the dyes were also investigated, and their application on polyester fabric showed excellent color yield and fastness properties.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
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
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
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
Multidisciplinary Sciences
Gaurav Goyal, Elina Ekedahl, My Nyblom, Jens Krog, Erik Frobrant, Magnus Brander, Tsegaye Sewunet, Teerawit Tangkoskul, Christian G. Giske, Linus Sandegren, Visanu Thamlikitkul, Tobias Ambjornsson, Fredrik Westerlund
Summary: Antimicrobial resistance is a growing threat to global health, and effective methods for detecting antimicrobial resistance genes on bacterial plasmids are necessary. In this study, researchers propose a simple and inexpensive assay based on CRISPR/Cas9 excision and DNA combing to detect these genes.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Evan S. H. Kang, K. K. Sriram, Inho Jeon, Jehan Kim, Shangzhi Chen, Kyoung-Ho Kim, Ka-Hyun Kim, Hyun Seok Lee, Fredrik Westerlund, Magnus P. Jonsson
Summary: Optical nanoantennas provide control of light at the nanoscale and have diverse applications. Traditional metallic and dielectric nanostructures can only support plasmonic and Mie resonances, respectively, while nanostructures of organic J-aggregate excitonic materials can support both plasmon-like resonances and dielectric resonances. These structures are highly anisotropic, enabling them to support hyperbolic localized surface exciton resonances and elliptic Mie resonances.
Article
Multidisciplinary Sciences
Tsegaye Sewunet, K. K. Sriram, Ha Hoang Nguyen, Noikaseumsy Sithivong, Ngoc Thi Bich Hoang, Vanphanom Sychareun, Kokasia Nengmongvang, Mattias Larsson, Linus Olson, Fredrik Westerlund, Christian G. Giske
Summary: In this study, the colonization rate of carbapenemase-producing Enterobacterales (CPE) on admission to intensive care units in Vientiane, Lao PDR was determined. The prevalence of extended-spectrum beta-lactamases (ESBLs) was high, while carbapenemases were less common. However, clonal dissemination of bla(NDM-1)-producing Klebsiella pneumoniae isolates in one of the intensive care units was detected, highlighting the need for stringent infection prevention and antimicrobial stewardship strategies.
Review
Biophysics
Karolin Frykholm, Vilhelm Muller, K. K. Sriram, Kevin D. Dorfman, Fredrik Westerlund
Summary: Nanofluidic structures provide a powerful platform for detailed analysis of DNA. By confining DNA to nanochannels, it can be stretched to near its full length without any chemical modifications. The versatility of nanofabrication allows for the design of devices tailored for specific applications, such as controlling confinement or enabling exchange of reagents. The two important applications discussed in this review are optical DNA mapping and DNA-protein interactions, showcasing the power of DNA confinement and nanofluidics in genomics, molecular biology, and biophysics.
QUARTERLY REVIEWS OF BIOPHYSICS
(2022)
Article
Multidisciplinary Sciences
Sagar Mahale, Meenakshi Setia, Bharat Prajapati, Santhilal Subhash, Mukesh Pratap Yadav, Subazini Thankaswamy Kosalai, Ananya Deshpande, Jagannath Kuchlyan, Mirco Di Marco, Fredrik Westerlund, L. Marcus Wilhelmsson, Chandrasekhar Kanduri, Meena Kanduri
Summary: The study reveals the critical role of HnRNPK in regulating double-stranded RNA formation in loci with overlapping sense and antisense transcripts, maintaining them in a single-stranded form and determining their oncogenic functions through blocking RNA-RNA interactions.
NATURE COMMUNICATIONS
(2022)
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)