Pub Date : 2025-05-26DOI: 10.1016/j.mocell.2025.100233
Seungjae Hwang, Jongsun Lee, Seung-Jae V. Lee
Assessing health parameters is essential for understanding the decline of physiological functions during aging. The nematode Caenorhabditis elegans serves as a powerful model in aging research. This paper introduces representative methods for evaluating health parameters using C. elegans and provides quantitative indicators of functional declines during aging. This manuscript will be useful for researchers unfamiliar with healthspan studies using C. elegans and may help perform physiological experiments for healthy aging.
{"title":"Brief guide to assays for measuring health parameters using Caenorhabditis elegans","authors":"Seungjae Hwang, Jongsun Lee, Seung-Jae V. Lee","doi":"10.1016/j.mocell.2025.100233","DOIUrl":"10.1016/j.mocell.2025.100233","url":null,"abstract":"<div><div>Assessing health parameters is essential for understanding the decline of physiological functions during aging. The nematode <em>Caenorhabditis elegans</em> serves as a powerful model in aging research. This paper introduces representative methods for evaluating health parameters using <em>C. elegans</em> and provides quantitative indicators of functional declines during aging. This manuscript will be useful for researchers unfamiliar with healthspan studies using <em>C. elegans</em> and may help perform physiological experiments for healthy aging.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 8","pages":"Article 100233"},"PeriodicalIF":3.7,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-21DOI: 10.1016/S1016-8478(25)00052-4
{"title":"Cover and caption","authors":"","doi":"10.1016/S1016-8478(25)00052-4","DOIUrl":"10.1016/S1016-8478(25)00052-4","url":null,"abstract":"","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 6","pages":"Article 100228"},"PeriodicalIF":3.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144099297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-20DOI: 10.1016/j.mocell.2025.100223
Soyoung Kim , Mina Han , Hyun Ju Hwang , Young-Ho Ahn , Ho Joon Im , Sang-Hyun Hwang , Kyung-Nam Koh , Nayoung Kim
MicroRNAs (miRNAs) are key regulators of cancer pathogenesis, and their expression is often dysregulated in cancer cells. The role of miR-196a-5p has been investigated in various types of cancers. However, it is relatively less understood in B-cell malignancies. This study aimed to investigate the role of miR-196a-5p in B cells by using a human diffuse large B-cell lymphoma cell line, SU-DHL-6, and mouse B lymphocytes. The enforced expression of miR-196a in SU-DHL-6 cells increased daunorubicin-mediated apoptosis. Luciferase assay revealed that FOXO1 was a direct target of miR-196a-5p in SU-DHL-6 cells. The mRNA and protein expression of FOXO1 was downregulated in miR-196a-overexpressing SU-DHL-6 cells. In addition, miR-196a-5p was highly expressed in mouse bone marrow cells, compared with that of splenic B cells, and FOXO1 expression was negatively correlated with miR-196a-5p level. miR-196a-5p was upregulated by B-cell receptor stimulation, which was inversely correlated with FOXO1 expression in splenic B cells. Apoptosis was increased when miR-196a-5p was upregulated in murine primary B cells. These results identify miR-196a-5p as a post-transcriptional regulator of FOXO1 and indicate its importance in regulating B-cell malignancies and activation.
{"title":"MicroRNA-196a increases apoptosis in B cells through downregulation of FOXO1","authors":"Soyoung Kim , Mina Han , Hyun Ju Hwang , Young-Ho Ahn , Ho Joon Im , Sang-Hyun Hwang , Kyung-Nam Koh , Nayoung Kim","doi":"10.1016/j.mocell.2025.100223","DOIUrl":"10.1016/j.mocell.2025.100223","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) are key regulators of cancer pathogenesis, and their expression is often dysregulated in cancer cells. The role of miR-196a-5p has been investigated in various types of cancers. However, it is relatively less understood in B-cell malignancies. This study aimed to investigate the role of miR-196a-5p in B cells by using a human diffuse large B-cell lymphoma cell line, SU-DHL-6, and mouse B lymphocytes. The enforced expression of miR-196a in SU-DHL-6 cells increased daunorubicin-mediated apoptosis. Luciferase assay revealed that FOXO1 was a direct target of miR-196a-5p in SU-DHL-6 cells. The mRNA and protein expression of FOXO1 was downregulated in miR-196a-overexpressing SU-DHL-6 cells. In addition, miR-196a-5p was highly expressed in mouse bone marrow cells, compared with that of splenic B cells, and FOXO1 expression was negatively correlated with miR-196a-5p level. miR-196a-5p was upregulated by B-cell receptor stimulation, which was inversely correlated with FOXO1 expression in splenic B cells. Apoptosis was increased when miR-196a-5p was upregulated in murine primary B cells. These results identify miR-196a-5p as a post-transcriptional regulator of FOXO1 and indicate its importance in regulating B-cell malignancies and activation.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 7","pages":"Article 100223"},"PeriodicalIF":3.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-20DOI: 10.1016/j.mocell.2025.100224
Soyeong An , Youngseo Kim , Ja Yil Lee
The advancement of single-molecule imaging techniques has significantly enhanced our understanding of biomolecular reactions and cellular processes that remain obscured in ensemble measurements. In particular, DNA curtains are high-throughput hybrid methods integrating total internal reflection fluorescence microscopy, lipid fluidity, microfluidics, and nano-fabrication, enabling the direct visualization of protein-DNA interactions in real time. The techniques have emerged as powerful tools for probing molecular dynamics of diverse DNA metabolic processes, including DNA damage repair and chromatin dynamics. This review not only highlights recent applications of DNA curtain techniques for elucidating mechanisms underlying DNA damage repair and chromatin dynamics, but also shows how DNA curtain techniques have provided novel insights into the interplay between DNA metabolic processes in the chromatin context.
{"title":"A novel high-throughput single-molecule technique DNA curtain: Applications for DNA metabolism","authors":"Soyeong An , Youngseo Kim , Ja Yil Lee","doi":"10.1016/j.mocell.2025.100224","DOIUrl":"10.1016/j.mocell.2025.100224","url":null,"abstract":"<div><div>The advancement of single-molecule imaging techniques has significantly enhanced our understanding of biomolecular reactions and cellular processes that remain obscured in ensemble measurements. In particular, DNA curtains are high-throughput hybrid methods integrating total internal reflection fluorescence microscopy, lipid fluidity, microfluidics, and nano-fabrication, enabling the direct visualization of protein-DNA interactions in real time. The techniques have emerged as powerful tools for probing molecular dynamics of diverse DNA metabolic processes, including DNA damage repair and chromatin dynamics. This review not only highlights recent applications of DNA curtain techniques for elucidating mechanisms underlying DNA damage repair and chromatin dynamics, but also shows how DNA curtain techniques have provided novel insights into the interplay between DNA metabolic processes in the chromatin context.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 7","pages":"Article 100224"},"PeriodicalIF":3.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-20DOI: 10.1016/j.mocell.2025.100225
Chanyoung Lee , Jin Sook Lee , Yejin Kwon , Aeri Shin , Tae Yeong Jeong , Jiyun Yang , Jung Woo Hwang , Hyeong-In Kim , Hee-Jung Choi , Yoon Ki Kim , Murim Choi , Kyoungmi Kim , Woong Sun , Jong-Hee Chae
Nonsense-mediated mRNA decay (NMD) eliminates transcripts containing premature termination codons, thereby preventing errors in protein synthesis. Serine/threonine-protein kinase SMG1 is a crucial kinase for NMD response, interacting with other regulatory proteins such as SMG8 and SMG9. We identified a de novo heterozygous variant in SMG1 p.Gln2398Glu (c.7192C>G) in a patient with global developmental delay, facial dysmorphism, and oculomotor apraxia. Thus, stem cell models with SMG1 mutations using gene editing technology were established to address the functional consequences of this mutation. While mutations causing the reduction in SMG1 gene dosage by alterations in splicing (c.7192_7194delinsGAA; GAA/+) or frameshift (c.4331_4337del; KO/+) led to a mild but significant reduction of NMD activity, NMD activity was not altered in cells with the SMG1 GAG/+ mutation. Furthermore, cortical organoids from hPSCGAA/+ exhibited size reduction compared with the control (CTL) or GAG/+, suggesting that reduced NMD activity can affect nervous system development. These findings suggest that hypomorphic SMG1 mutations can cause reduced NMD activity and subsequent biological responses, while the mutation found in the patient alone may not be sufficient to induce pathological symptoms.
{"title":"Effects of heterozygous SMG1 mutations on nonsense-mediated mRNA decay in human pluripotent stem cell model","authors":"Chanyoung Lee , Jin Sook Lee , Yejin Kwon , Aeri Shin , Tae Yeong Jeong , Jiyun Yang , Jung Woo Hwang , Hyeong-In Kim , Hee-Jung Choi , Yoon Ki Kim , Murim Choi , Kyoungmi Kim , Woong Sun , Jong-Hee Chae","doi":"10.1016/j.mocell.2025.100225","DOIUrl":"10.1016/j.mocell.2025.100225","url":null,"abstract":"<div><div>Nonsense-mediated mRNA decay (NMD) eliminates transcripts containing premature termination codons, thereby preventing errors in protein synthesis. Serine/threonine-protein kinase SMG1 is a crucial kinase for NMD response, interacting with other regulatory proteins such as SMG8 and SMG9. We identified a de novo heterozygous variant in <em>SMG1</em> p.Gln2398Glu (c.7192C>G) in a patient with global developmental delay, facial dysmorphism, and oculomotor apraxia. Thus, stem cell models with <em>SMG1</em> mutations using gene editing technology were established to address the functional consequences of this mutation. While mutations causing the reduction in <em>SMG1</em> gene dosage by alterations in splicing (c.7192_7194delinsGAA; GAA/+) or frameshift (c.4331_4337del; KO/+) led to a mild but significant reduction of NMD activity, NMD activity was not altered in cells with the <em>SMG1</em> GAG/+ mutation. Furthermore, cortical organoids from hPSC<sup>GAA/+</sup> exhibited size reduction compared with the control (CTL) or GAG/+, suggesting that reduced NMD activity can affect nervous system development. These findings suggest that hypomorphic <em>SMG1</em> mutations can cause reduced NMD activity and subsequent biological responses, while the mutation found in the patient alone may not be sufficient to induce pathological symptoms.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 7","pages":"Article 100225"},"PeriodicalIF":3.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-08DOI: 10.1016/j.mocell.2025.100222
Byeong Seob Oh , Juhee Kim , Minjeong Kwon , Jiwon Bang , Kwang-Jun Lee , Eun-Jin Lee , Yong-Joon Cho
Large-scale datasets are central to bioinformatics research, creating a demand for intuitive visualization tools that transform complex data into accessible graphics. Existing visualization software often comes with high costs or requires coding expertise, limiting accessibility for many researchers. To address this gap, we introduce SimpleViz, a free, web-based platform that enables the creation of professional-quality figures without the need for programming skills. SimpleViz offers gene-level analysis of RNA-seq data and core visualization types such as box/violin/dot plots, volcano plots, principal component analysis plots, and heatmaps, with extensive customization options for detailed adjustments and built-in statistical comparisons. Developed on a Shiny interface, SimpleViz simplifies the process of data upload, visualization generation, and customization, ensuring that users can produce tailored visuals suited for publication. With plans for continuous improvement based on user feedback, SimpleViz provides an adaptable, accessible solution that meets evolving data analysis needs in biomedical research.
{"title":"SimpleViz: A user-friendly, web-based tool for publication-ready data visualization in bioinformatics","authors":"Byeong Seob Oh , Juhee Kim , Minjeong Kwon , Jiwon Bang , Kwang-Jun Lee , Eun-Jin Lee , Yong-Joon Cho","doi":"10.1016/j.mocell.2025.100222","DOIUrl":"10.1016/j.mocell.2025.100222","url":null,"abstract":"<div><div>Large-scale datasets are central to bioinformatics research, creating a demand for intuitive visualization tools that transform complex data into accessible graphics. Existing visualization software often comes with high costs or requires coding expertise, limiting accessibility for many researchers. To address this gap, we introduce SimpleViz, a free, web-based platform that enables the creation of professional-quality figures without the need for programming skills. SimpleViz offers gene-level analysis of RNA-seq data and core visualization types such as box/violin/dot plots, volcano plots, principal component analysis plots, and heatmaps, with extensive customization options for detailed adjustments and built-in statistical comparisons. Developed on a Shiny interface, SimpleViz simplifies the process of data upload, visualization generation, and customization, ensuring that users can produce tailored visuals suited for publication. With plans for continuous improvement based on user feedback, SimpleViz provides an adaptable, accessible solution that meets evolving data analysis needs in biomedical research.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 7","pages":"Article 100222"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-25DOI: 10.1016/j.mocell.2025.100221
Thilini Ranasinghe , Seon-Heui Cha
This work described simple methods for measuring locomotive activity using open-source software, ImageJ1.54fFiji, and VirtualDub2. The significance of animal behavior is a mirror of brain activity, which can give information implicated with neurological diseases. Commercial behavioral analysis software frequently needs expertise and expenses high costs due to equip a specific instrument to use of software, thereby encouraging a trend toward open-source alternatives that are both accessible and effective. Here, we explained how to convert video format, measure movement, and produce useful locomotive parameters to aid in the assessment of zebrafish embryos. This method could be easily translated for use in other model systems. This methodology seeks to streamline behavioral quantification in research contexts, encouraging broader research aspects.
{"title":"Open-source software utilization for zebrafish embryos behavior test","authors":"Thilini Ranasinghe , Seon-Heui Cha","doi":"10.1016/j.mocell.2025.100221","DOIUrl":"10.1016/j.mocell.2025.100221","url":null,"abstract":"<div><div>This work described simple methods for measuring locomotive activity using open-source software, ImageJ1.54fFiji, and VirtualDub2. The significance of animal behavior is a mirror of brain activity, which can give information implicated with neurological diseases. Commercial behavioral analysis software frequently needs expertise and expenses high costs due to equip a specific instrument to use of software, thereby encouraging a trend toward open-source alternatives that are both accessible and effective. Here, we explained how to convert video format, measure movement, and produce useful locomotive parameters to aid in the assessment of zebrafish embryos. This method could be easily translated for use in other model systems. This methodology seeks to streamline behavioral quantification in research contexts, encouraging broader research aspects.</div></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 6","pages":"Article 100221"},"PeriodicalIF":3.7,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-21DOI: 10.1016/S1016-8478(25)00041-X
{"title":"Cover and caption","authors":"","doi":"10.1016/S1016-8478(25)00041-X","DOIUrl":"10.1016/S1016-8478(25)00041-X","url":null,"abstract":"","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":"48 5","pages":"Article 100217"},"PeriodicalIF":3.7,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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