Review
Cell Biology
Ashwini Shinde, Kavitha Illath, Pallavi Gupta, Pallavi Shinde, Ki-Taek Lim, Moeto Nagai, Tuhin Subhra Santra
Summary: Cells exert, sense, and respond to physical forces through diverse mechanisms, translating them into biochemical signals. Cell adhesion plays a crucial role in development, maintaining tissue morphogenesis and activating critical signaling pathways. Understanding cell adhesion regulation during development and its contribution to diseases with quantitative methods is essential.
Article
Medicine, Research & Experimental
Catriona T. Prendergast, Robert A. Benson, Hannah E. Scales, Caio Santos Bonilha, John J. Cole, Iain McInnes, James M. Brewer, Paul Garside
Summary: This study used mouse models and RNA-Seq analysis to identify key molecular pathways and genes regulating immune cell migration, and discovered specific genes associated with rheumatoid arthritis. The findings are important for identifying therapeutic targets for arthritis and other inflammatory disorders.
Article
Biochemistry & Molecular Biology
Xue Qiao, Conghui Liu, Weilin Wang, Chuanyan Yang, Meijia Li, Qilin Yi, Ning Kong, Limei Qiu, Xiyang Liu, Lingling Wang, Linsheng Song
Summary: Neural cell adhesion molecules (NCAMs) are large cell-surface glycoproteins that play important roles in cell-cell and cell-extracellular matrix interactions in the nervous system. A recent study identified a homologue of NCAM (CgNCAM) in the Pacific oyster Crassostrea gigas. CgNCAM was found to be widely distributed in oyster tissues, particularly in the mantle, labial palp, and haemolymph. It showed increased expression in oyster haemocytes after stimulation with Vibrio splendidus and Staphylococcus aureus.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Pathology
Anna L. Gray, Nabina Pun, Amanda J. L. Ridley, Douglas P. Dyer
Summary: Leucocyte recruitment is crucial in the immune response and inflammatory diseases. The role of proteoglycans in this process has been underestimated. Proteoglycans bind and regulate the function of proteins, such as chemokines, and also have structural roles in tissue environments. Understanding the mechanistic role of proteoglycans in inflammatory diseases is important for developing new therapeutics.
INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY
(2022)
Article
Multidisciplinary Sciences
Uiyoung Han, Wijin Kim, Hyeonjin Cha, Ju Hyun Park, Jinkee Hong
Summary: The method of engineering the iPSC membrane to stimulate the inner cells of EBs while preserving cellular activities is reported in this study. The nano-coating on iPSCs allows them to retain their properties such as adhesion capability, proliferation, and pluripotency during aggregation, without inducing lineage-specific differentiation but increasing E-cadherin expression to promote EB development. This provides a foundation for future production of sophisticated patient-specific multicellular aggregates through modification of living cell membranes.
Review
Developmental Biology
Naoya Yamaguchi, Holger Knaut
Summary: Cell-extracellular matrix interactions are essential for cell anchoring and migration, with focal adhesions (FAs) playing a key role. However, the role of FAs in vivo is still not well understood.
Article
Chemistry, Multidisciplinary
Siying Li, Xuelei Pang, Jing Zhao, Qingrong Zhang, Yuping Shan
Summary: Targeted peptides are important in the construction of intelligent drug delivery systems, and the interaction between peptides and receptors is crucial for the efficacy of targeted nano-drugs. Using single-molecule force spectroscopy, this study evaluated the stability and effectiveness of three common peptides targeting specific receptors on living cell surfaces. The T7-TfR bond was found to be the most stable among the three peptide-receptor pairs.
Article
Multidisciplinary Sciences
Janett Goehring, Florian Kellner, Lukas Schrangl, Rene Platzer, Enrico Klotzsch, Hannes Stockinger, Johannes B. Huppa, Gerhard J. Schuetz
Summary: This study introduces a FRET-based sensor that directly measures the magnitude and kinetics of forces imposed by TCR at the single molecule level. Results showed that when T cells were confronted with gel-phase SLBs, there was a single force peak of around 5pN prior and upon activation, with force loading rates around 1.5pN per second on the TCR; while facing fluid-phase SLBs, T cells exerted tensile forces prior to activation but not afterwards, although of reduced magnitude compared to gel-phase SLBs.
NATURE COMMUNICATIONS
(2021)
Article
Medicine, Research & Experimental
Chandan Sona, Yu-Te Yeh, Andreas Patsalos, Laszlo Halasz, Xin Yan, Natalia L. Kononenko, Laszlo Nagy, Matthew N. Poy
Summary: Through single-cell RNA sequencing analysis, this study found increased CADM1(+) cells adjacent to CD8(+) T cells in the islets of individuals with T1D and those who were autoantibody-positive, indicating that CADM1-mediated intercellular contact may facilitate the infiltration of cytotoxic T lymphocytes and could serve as a potential therapeutic target for preventing T1D pathogenesis.
Article
Multidisciplinary Sciences
Anouk Mentink, Khrystany T. Isebia, Jaco Kraan, Leon W. M. M. Terstappen, Michiel Stevens
Summary: When evaluating EpCAM-based enrichment technologies for CTCs, it is important to use cell lines that closely resemble real CTCs and measure the EpCAM expression of both CTCs and cell lines at different institutions and times. In this study, CTCs were enriched by depleting leukocytes from diagnostic leukapheresis products and EpCAM expression was measured using quantitative flow cytometry. Results showed varying but relatively low EpCAM expression in CTCs from castration-sensitive prostate cancer patients. There were also significant variations in antigen expression among identical cell lines cultured at different institutions, affecting capture efficiency.
SCIENTIFIC REPORTS
(2023)
Review
Cell Biology
Timoteo Marchini, Lucia Sol Mitre, Dennis Wolf
Summary: Atherosclerosis is a chronic inflammatory disease initiated and maintained by leukocytes, which can lead to myocardial infarction and stroke. Challenges in developing therapies for leukocyte accumulation include the lack of tissue-tropism of targeted factors and unspecific inhibition strategies.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Qian-Yue Zhang, Xiao-Ping Ye, Zheng Zhou, Chen-Fang Zhu, Rui Li, Ya Fang, Rui-Jia Zhang, Lu Li, Wei Liu, Zheng Wang, Shi-Yang Song, Sang-Yu Lu, Shuang-Xia Zhao, Jian-Nan Lin, Huai-Dong Song
Summary: By using single-cell RNA sequencing, this study reveals the presence of three stromal cell subtypes in the thyroidal microenvironment of Hashimoto's Thyroiditis, which may contribute to the recruitment of inflammatory immune cells. The study provides a deeper insight into the cellular interactions that might prompt the pathogenesis of Hashimoto's Thyroiditis.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Taichi Matsumoto, Junichi Matsumoto, Yuka Matsushita, Moeno Arimura, Kentaro Aono, Mikiko Aoki, Kazuki Terada, Masayoshi Mori, Yutaka Haramaki, Takuya Imatoh, Atsushi Yamauchi, Keisuke Migita
Summary: This study investigated the effect of bortezomib (BTZ) on vascular permeability and expression of cell-cell junction molecules in human pulmonary microvascular endothelial cells. The findings showed that clinically relevant concentrations of BTZ increased the permeability of endothelial cell monolayers and downregulated the expression of claudin-5, occludin, and VE-cadherin at both protein and mRNA levels. This suggests that BTZ-induced pulmonary toxicity may be mediated by increased vascular permeability caused by the downregulation of these cell-cell junction molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Sara A. Rubin, Chloe S. Baron, Cecilia Pessoa Rodrigues, Madeleine Duran, Alexandra F. Corbin, Song P. Yang, Cole Trapnell, Leonard I. Zon
Summary: This study provides insights into key aspects of zebrafish lymphocyte development and cellular diversity through single-cell RNA sequencing. It advances the understanding of zebrafish immunology and will facilitate future genetic and developmental studies.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Review
Biology
M. Shahid Mansuri, Kenneth Williams, Angus C. Nairn
Summary: Recent technological advances have enabled single-cell proteomics to unravel the role of protein expression, post-translational modifications, and protein interactions in determining cell state in both health and disease.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shin-ichi Yamazaki, Hidenori Hashimura, Yusuke Morimoto, Yukihiro Miyanaga, Satomi Matsuoka, Yoichiro Kamimura, Masahiro Ueda
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Cell Biology
Haruka Hiraoka, Tadashi Nakano, Satoshi Kuwana, Masashi Fukuzawa, Yasuhiro Hirano, Masahiro Ueda, Tokuko Haraguchi, Yasushi Hiraoka
Article
Multidisciplinary Sciences
Nange Jin, Zhijing Zhang, Joyce Keung, Sean B. Youn, Munenori Ishibashi, Lian-Ming Tian, David W. Marshak, Eduardo Solessio, Yumiko Umino, Iris Fahrenfort, Takae Kiyama, Chai-An Mao, Yanan You, Haichao Wei, Jiaqian Wu, Friso Postma, David L. Paul, Stephen C. Massey, Christophe P. Ribelayga
Article
Biochemistry & Molecular Biology
Daisuke Ohtsuka, Nobutoshi Ota, Satoshi Amaya, Satomi Matsuoka, Yo Tanaka, Masahiro Ueda
Summary: The study found that chemotaxis was strongest at a cAMP concentration of 100 nM, with about 16% of cells still exhibiting chemotaxis at a concentration of 10 pM. Additionally, chemotaxis was suppressed at a concentration of 100 pM cAMP due to the self-production and secretion of intracellular cAMP induced by extracellular cAMP.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Neurosciences
Christopher M. Whitaker, Gina Nobles, Munenori Ishibashi, Stephen C. Massey
Summary: Rod and cone pathways are initially segregated in the retina, but there is evidence of some crossover connections between the two pathways. Physiological recordings suggest that rod bipolar cells can receive input from cones, and ON cone bipolar cells may also receive input from rods. Imaging studies show that some rod bipolar cells have cone contacts, while tertiary rod pathways operate via direct contacts between rods and OFF cone bipolar cells. However, no evidence was found for rod contacts with ON cone bipolar cells in the rabbit retina.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Biochemical Research Methods
Takeru Kameda, Katsura Asano, Yuichi Togashi
Summary: This study introduces a new method to evaluate free energy profiles by computing the distance between base-pairs in the recognition of start codons in eukaryotic translation pre-initiation complex. It reveals how a G:U mismatch affects the accommodation of start codons in the initiating ribosome, and demonstrates that initiation at a CUG codon is nearly as strong as, or sometimes stronger than, that at a GUG codon.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Naoyuki Kawase, Atsuya Sugihara, Kentaro Kajiwara, Michio Hiroshima, Kanako Akamatsu, Shigeyuki Nada, Kunio Matsumoto, Masahiro Ueda, Masato Okada
Summary: The CDCP1-SRC-ARHGEF7-RAC1 pathway plays a crucial role in HGF-induced invasion of a subset of breast cancer cells.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biology
Munenori Ishibashi, Joyce Keung, Catherine W. Morgans, Sue A. Aicher, James R. Carroll, Joshua H. Singer, Li Jia, Wei Li, Iris Fahrenfort, Christophe P. Ribelayga, Stephen C. Massey
Summary: Electrical coupling mediated by gap junctions plays a crucial role in signal averaging, synchronization, and noise reduction in neuronal circuits. This study successfully reconstructed gap junctions between photoreceptors in the mouse retina using a combination of electron microscopy techniques, shedding light on the distribution and function of Cx36 at these sites.
Article
Multidisciplinary Sciences
Yoshihiko Fujita, Takeru Kameda, Chingakham Ranjit Singh, Whitney Pepper, Ariana Cecil, Madelyn Hilgers, Mackenzie Thornton, Izumi Asano, Carter Moravek, Yuichi Togashi, Hirohide Saito, Katsura Asano
Summary: This study reveals that the combined modification of 5-cytosine methylation and pseudouridylation can enhance the initiation frequencies of GUG and UUG start codons in eukaryotes, making them more favorable than CUG initiation. Molecular dynamics simulations show that this modification increases the affinity between modified codons and tRNA, mitigating the discrimination against non-AUG codons. These findings suggest that chemical modifications of start codon bases can provide a new mechanism for regulating proteome diversity and therapeutic mRNA technology.
Article
Cell Biology
Kazutoshi Takebayashi, Yoichiro Kamimura, Masahiro Ueda
Summary: In this study, the lateral diffusion of transmembrane proteins in Dictyostelium discoideum cells was systematically investigated. It was found that transmembrane proteins exhibited three free diffusion states with similar diffusion coefficients regardless of their structural variability. In addition, the mobility of all protein species decreased upon the inhibition of microtubule or actin cytoskeleton dynamics, or myosin II. The relationship between protein size and diffusion coefficient was consistent with the Saffman-Delbru' ck model, indicating that membrane viscosity is a major determinant of lateral diffusion.
JOURNAL OF CELL SCIENCE
(2023)
Review
Biophysics
Takeru Kameda, Akinori Awazu, Yuichi Togashi
Summary: This review summarizes the recent progress in studying the structural dynamics of nucleic acid molecules in the context of gene regulation. It highlights the importance of the physicochemical properties of nucleotides and amino acids in understanding the structure-function relationship. The review also points out the relatively underdeveloped field of molecular simulation of nucleic acids and calls for closer collaboration between experimentalists and computational biologists.
BIOPHYSICS AND PHYSICOBIOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Takeru Kameda, Miho M. Suzuki, Akinori Awazu, Yuichi Togashi
Summary: DNA methylation is associated with biological phenomena and epigenetic regulation, and can alter the mechanical properties of DNA molecules. This study used molecular dynamics simulations to show that methylation patterns affect the local flexibility of DNA, ultimately impacting its overall geometry and stiffness. These findings provide insights into methylation-dependent DNA dynamics in physiological conditions.
Article
Genetics & Heredity
Soya Shinkai, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, Shuichi Onami
NAR GENOMICS AND BIOINFORMATICS
(2020)
Article
Biology
Daisuke Yoshioka, Seiya Fukushima, Hiroyasu Koteishi, Daichi Okuno, Toru Ide, Satomi Matsuoka, Masahiro Ueda
COMMUNICATIONS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
