Editorial Material
Biochemistry & Molecular Biology
Adam M. M. Stuckert, Daniel R. Matute
Summary: Wolbachia, a globally distributed endosymbiotic bacteria, can be found in numerous species of arthropods and nematodes. The frequency of one strain, wMel, varies significantly worldwide. Hague et al. have discovered that the variation of wMel in nature can be explained by the interaction of host genotype, symbiont genotype, and environment.
Article
Chemistry, Physical
Stefan Milenkovic, Jiajun Wang, Silvia Acosta-Gutierrez, Mathias Winterhalter, Matteo Ceccarelli, Igor V. Bodrenko
Summary: Transmembrane beta-barrel proteins are versatile candidates for various technological applications and their behavior is influenced by environmental conditions. Comparing two highly homologous porins, OmpF and OmpC, we observed subtle amino acid substitutions that can modulate mass transport properties. These differences can be attributed to the disparities in the environmental conditions under which the porins are expressed. Our analysis not only highlights the advantages of enhanced sampling methods, but also provides valuable insights into the biological function and technical applications of these proteins.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Kaikai Chen, Ining Jou, Niklas Ermann, Murugappan Muthukumar, Ulrich F. Keyser, Nicholas A. W. Bell
Summary: Studying polymer translocation through synthetic nanopores reveals a two-stage behavior, where the translocation initially slows before accelerating close to the end of the process, with distinct local velocity correlations observed as the DNA polymer chain passes through the nanopore. Brownian dynamics simulations show that this behavior is associated with tension propagation, providing a non-equilibrium description of the process.
Article
Environmental Sciences
Lucia Ivorra, Catarina Cruzeiro, Alice Ramos, Karen Tagulao, Patricia G. Cardoso
Summary: The study showed that the edible clam Meretrix meretrix did not exhibit significant DNA damage under dicofol exposure, possibly due to optimal adaptation to stress conditions or the lack of genotoxicity of dicofol. Moreover, all treatment groups showed an increase in DNA damage after exposure to ex vivo hydrogen peroxide, with the D1 group having significantly lower DNA damage during the uptake phase, indicating higher protection against a second stressor. These findings highlight the importance of organisms' origin and their exposure conditions in determining their response to genotoxic agents.
ENVIRONMENTAL POLLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Agnieszka Ludwiczak, Ewa Skrzypczak, Joanna Skladanowska-Baryza, Marek Stanisz, Piotr Slosarz, Przemyslaw Racewicz
Summary: The increasing interest in the welfare of farmed animals has led to the development of alternative production systems for pigs, with outdoor housing considered beneficial for allowing pigs to display natural behaviors. However, outdoor systems also come with drawbacks such as increased risk of injuries.
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
Biochemistry & Molecular Biology
Venkataharsha Panuganti, Ipsita Roy
Summary: The classical Hofmeister series orders ions into kosmotropes and chaotropes based on their interaction with water, but recent studies suggest that the interaction with proteins can also play a significant role. Intrinsically disordered proteins (IDPs) have different characteristics compared to globular proteins, such as different amino acid compositions and lack of distinct secondary and tertiary structures. Different ions have different effects on the compactness of protein conformations, and can either promote or inhibit protein aggregation. The traditional classification of molecules into protein stabilizers and destabilizers needs to be reassessed for IDPs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Swarnadeep Seth, Aniket Bhattacharya
Summary: High fidelity DNA capture is essential for nanopore translocation. This study investigates the capture process and subsequent translocation of DNA through a solid-state nanopore using Brownian dynamics simulation. The study finds that the field gradient elongates DNA and improves the success rate of translocation. It also shows that even in a narrow pore, there is a probability of hairpin-loop capture. Additionally, the study discovers that a charged tag attached to the 5' end of DNA enhances the multi-scan rate and the probability of uni-directional translocation.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Analytical
Lohra M. Miller, Benjamin E. Draper, Lauren F. Barnes, Polycarp C. Ofoegbu, Martin F. Jarrold
Summary: Conventional mass spectrometry of nucleic acids is complicated by counter ions, limiting the analysis of DNA size. This study overcomes this limitation using charge detection mass spectrometry to analyze megadalton-sized DNA. Different charge distributions are observed for DNA plasmids, with a low-charge population resembling compact DNA and a higher-charge population with a broad charge range. The high-charge population is attributed to supercoiled plasmids in random coil configuration, while the low-charge population is attributed to a condensed form of the plasmid.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Longfu Xu, Matthew T. J. Halma, Gijs J. L. Wuite
Summary: Single-stranded DNA-binding proteins (SSBs) are essential for DNA metabolism and play crucial roles in maintaining genome integrity and coordinating with other proteins involved in DNA replication, recombination, and repair. Recent advances in single-molecule techniques and structural methods have greatly improved our understanding of the binding dynamics and interaction of SSBs with ssDNA and other protein partners. We highlight the central coordination role of SSBs in directly modulating the activities of other proteins and discuss the various modes of interaction between SSBs and their protein partners, providing a comprehensive view of the interaction network shaped by SSBs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Miriam Simon, Albert Prause, Stefan Zauscher, Michael Gradzielski
Summary: This study investigates the directed self-assembly of complementary single-stranded DNA strands (poly(dA) and poly(dT)) into complex, organized, and percolating networks in dilute solutions and at surfaces. The knowledge of DNA assemblies in solution and their impact on network formation is crucial for controlling the fabrication of nanotechnological devices. Fluorescence cross-correlation spectroscopy confirms the presence of larger DNA complexes in mixed solutions at low concentrations, emphasizing the importance of considering network precursors in solution.
Article
Multidisciplinary Sciences
Mingxuan Sun, Hossein Amiri, Alexander B. Tong, Keishi Shintomi, Tatsuya Hirano, Carlos Bustamante, Rebecca Heald
Summary: This study used a physiological, cell-free system to investigate the real-time formation and disassembly of mitotic chromatin fibers. The findings suggest that the core histone chaperone ASF1 and linker histone H1 play important roles in mitotic DNA compaction. The metaphase extract, compared to the interphase extract, showed a greater ability to compact DNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Nanoscience & Nanotechnology
S. M. Leitao, V. Navikas, H. Miljkovic, B. Drake, S. Marion, G. Pistoletti Blanchet, K. Chen, S. F. Mayer, U. F. Keyser, A. Kuhn, G. E. Fantner, A. Radenovic
Summary: In current nanopore-based label-free single-molecule sensing technologies, stochastic processes make it challenging to control the selection, rate, and velocity of single-molecule translocations. This study proposes a method that uses a glass nanopore mounted on a three-dimensional nanopositioner to spatially select and deterministically translocate molecules tethered on a glass surface. By controlling the distance between the nanopore and glass surface, the region of interest on the molecule can be actively selected and scanned at a controlled number of times and velocity. The method demonstrates versatility in assessing DNA-protein complexes, DNA rulers, and DNA gaps, enabling single-nucleotide gap detection.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Yang Du, Ying Lai, Ji-Yan Liu, Jiajie Diao
Summary: This article presents a new ultrasensitive method for detecting 5hmC modification in DNA, which requires a minimal amount of DNA sample and can provide results within a short period of time.
Article
Green & Sustainable Science & Technology
Dong Li, Guanfeng An, Xiangsheng Chen, Wengang Dang, Dongyang Li
Summary: This study proposes an experimental method to determine joint stiffness under constant normal load conditions and investigates the properties of normal and shear stiffness. The results show that joint normal and shear stiffness are time and spatially varying parameters, with normal stiffness being significantly higher than average shear stiffness. Shear velocity has little influence on average shear stiffness but affects instantaneous shear stiffness.
Article
Chemistry, Multidisciplinary
Hikari Baba, Risa Yoshioka, Satoshi Takatori, Yohei Oe, Kenichi Yoshikawa
Summary: A morphological transition was observed in the drying process of an aqueous solution containing glucose and starch, with changes from cracking of a 2D layer to peeling from the bottom layer as glucose content increased. The peeling film and remaining bottom layer were found to be rich in glucose and starch, respectively. A phenomenological nonlinear diffusion equation was proposed to explain the transition mechanism, including the effect of starch polymers on solidification. Numerical results with this equation successfully reproduced the essential features of the drying layer transition.
Article
Biochemistry & Molecular Biology
Tomoki Kitagawa, Takashi Nishio, Yuko Yoshikawa, Naoki Umezawa, Tsunehiko Higuchi, Chwen-Yang Shew, Takahiro Kenmotsu, Kenichi Yoshikawa
Summary: Polyamines play a role in various biological functions, with biphasic effects on gene expression observed at different concentrations. Among the naturally occurring tetravalent polyamines, thermospermine exhibits the strongest effects on DNA conformation and inhibition of gene expression activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Yuki Sugiura, Masahiro Okada, Ken Hirano, Takuya Matsumoto
Summary: This study demonstrates the excellent adhesion properties of octacalcium phosphate (OCP), a bioresorbable mineral analogue of immature bone, which can strongly adhere to biological soft tissues and exhibit antibacterial ability.
ADVANCED MATERIALS INTERFACES
(2021)
Article
Chemistry, Physical
Tatsuyuki Waizumi, Hiroki Sakuta, Masahito Hayashi, Kanta Tsumoto, Kingo Takiguchi, Kenichi Yoshikawa
Summary: This study investigated the impact of actin polymerization/depolymerization on water phase separation in a binary polymer solution. It was found that F-actin localized in the DEX-rich phase, and it took hours to restore homogeneous actin distribution after depolymerization by fragmin. When depolymerized actin was added to a solution with microphase separation, F-actin was found in non-spherical droplets, indicating an association between microphase separation and actin cytoskeleton dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Acoustics
Yue Ma, Kazuya Ishihara, Kenji Yoshida, Iwaki Akiyama, Kenichi Yoshikawa
Summary: The study found that exposure to ultrasound with sound pressure above a threshold value accelerated the increase in damage to DNA, with shorter pulse durations and longer pulse repetition periods causing more severe double-strand breaks. Additionally, a small amount of microbubbles was found to increase the damage to DNA, although this effect was weakly dependent on their concentrations.
JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Marcos K. Masukawa, Yusuke Sato, Fujio Yu, Kanta Tsumoto, Kenichi Yoshikawa, Masahiro Takinoue
Summary: This paper describes a purification method based on water-in-water droplet fractionation for separating excess components from self-assembled DNA nano/microstructures. The method is cost-effective and simple, and allows purification of structures with a broad size spectrum.
Article
Materials Science, Biomaterials
Takashi Nishio, Tomoya Masaoka, Yuko Yoshikawa, Koichiro Sadakane, Takahiro Kenmotsu, Helmut Schiessel, Kenichi Yoshikawa
Summary: The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system was studied using a luciferase assay. Rb+ was found to be the most efficient in promoting TX-TL, while Li+, Na+, and (CH3)(4)N+ exhibited inhibitory effects. Similar promotion/inhibition effects were observed in cell-free translation alone using an mRNA template.
Article
Biochemistry & Molecular Biology
Jekaterina Erenpreisa, Alessandro Giuliani, Kenichi Yoshikawa, Martin Falk, Georg Hildenbrand, Kristine Salmina, Talivaldis Freivalds, Ninel Vainshelbaum, Jonas Weidner, Aaron Sievers, Gotz Pilarczyk, Michael Hausmann
Summary: Complex functioning of the genome in the cell nucleus is controlled at different levels, including the DNA base sequence, epigenetic pathways, and genome architecture. This article reviews recent research on integrating these levels of genome expression regulation and discusses the conclusions from an international symposium held in Riga, Latvia, which addressed novel aspects of the topic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Polymer Science
Kohei Fujino, Takashi Nishio, Keita Fujioka, Yuko Yoshikawa, Takahiro Kenmotsu, Kenichi Yoshikawa
Summary: This report investigates the effects of alcohols on gene expression and the mechanical properties of DNA molecules. It shows that ethanol and 2-propanol significantly increase gene expression levels, while 1-propanol has an inhibitory effect. The observation of single DNA molecules reveals that 1-propanol greatly enhances the mechanical properties of DNA, while ethanol and 2-propanol have weaker effects. These findings demonstrate a correlation between the activation/inhibition effects of alcohol isomers on gene expression and the viscoelastic properties of DNA molecules.
Article
Biochemistry & Molecular Biology
Takashi Nishio, Yohji Shimada, Yuko Yoshikawa, Takahiro Kenmotsu, Helmut Schiessel, Kenichi Yoshikawa
Summary: In this study, we used an in vitro cell-free system with spermine to investigate the effect of daunomycin (DM) on gene expression. We found that DM exhibits a bimodal effect on gene expression, promoting at lower concentrations and inhibiting at higher concentrations. Through atomic force microscopy observation, we observed that DM destroys flower-like conformations of DNA induced by spermine, resulting in double-strand breaks. These newly revealed effects of DM on gene expression and DNA structure will contribute to the development and refinement of anticancer therapy chemicals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Multidisciplinary
Maho Kuroda, Satoshi Takatori, Takahiro Kenmotsu, Kenichi Yoshikawa, Chwen-Yang Shew
Summary: Macroscopic systems mimicking microscopic systems were used to study the organization of macro-molecules in a confined space. Experimental and numerical models showed that the behavior of a large particle interacting with small particles under different boundary conditions is influenced by crowding. Membrane stiffness was found to affect the organization of biopolymers and may play a role in cellular dynamics.
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN
(2023)
Article
Chemistry, Multidisciplinary
Mayu Shono, Gen Honda, Miho Yanagisawa, Kenichi Yoshikawa, Akihisa Shioi
Summary: In this study, a one-step method using glass capillaries and a polymer blend of PEG and gelatin is discussed for producing uniform cell-sized microgels. The method involves phase separation and gelation of the polymer blend upon decreasing temperature, leading to the formation of linearly aligned, uniformly sized gelatin microgels. The addition of DNA prevents coalescence of the microdroplets. This novel method has potential applications in biopolymers and cellular models.
Article
Chemistry, Multidisciplinary
Hiroki Sakuta, Naoki Nakatani, Takayuki Torisawa, Yutaka Sumino, Kanta Tsumoto, Kazuhiro Oiwa, Kenichi Yoshikawa
Summary: Water phase separation in cells can lead to mechanical motion by entrapping protein motors and generating vortex flow inside cell-sized droplets. This study reveals that the water phase separation interface can drive translational motion of droplets by spontaneously entrapping kinesins and microtubules and generating vortex flow. The findings highlight the importance of water phase separation in both chemical and mechanical processes.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Mayu Shono, Fumika Fujita, Kenichi Yoshikawa, Akihisa Shioi
Summary: Stable cell-sized droplets entrapping DNA molecules are generated through micro segregation. Measurements of electrification and Zeta potentials confirmed the presence of negatively charged droplets trapping the DNA.
Article
Physics, Fluids & Plasmas
Saori Suda, Tomoharu Suda, Takuya Ohmura, Masatoshi Ichikawa
Summary: This study investigates the effect of external perturbations on the motion of microdroplets driven by the Marangoni effect. The results show that the types and properties of external perturbation have a considerable impact on the droplet motion.