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Manipulation and analysis of large DNA molecules by controlling their dynamics using micro- and nano-gaps.
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-28 DOI: 10.1093/bbb/zbae179
Naoki Azuma
{"title":"Manipulation and analysis of large DNA molecules by controlling their dynamics using micro- and nano-gaps.","authors":"Naoki Azuma","doi":"10.1093/bbb/zbae179","DOIUrl":"https://doi.org/10.1093/bbb/zbae179","url":null,"abstract":"<p><p>Manipulation and analysis methods for large DNAs are critical for epidemiological, clinical, diagnostic, and fundamental research on bacteria, membrane vesicles, plants, yeast, and human cells. However, the physical properties of large DNAs often challenge their manipulation and analysis with high accuracy and speed using the conventional methods such as gel electrophoresis and column-based methods. This review presents the approaches that leverage micrometer- and nanometer-sized gaps within microchannels to control the dynamics and conformations of large DNAs, thereby overcoming these challenges. By designing gap structures and migration conditions based on the relationship between gap parameters and the physical characteristics of large DNAs-such as diameter and persistence length-these methods enable swifter and more precise manipulation and analysis of large DNAs, including size separation, concentration, purification, and single-molecule analysis.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Application of glucose to prepare Aspergillus oryzae koji as an adjunct to prevent rancidity in cheese products.
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-28 DOI: 10.1093/bbb/zbae174
Napaporn Chintagavongse, Tomohiro Mitani, Koichi Tamano, Toru Hayakawa, Jun-Ichi Wakamatsu, Haruto Kumura
{"title":"Application of glucose to prepare Aspergillus oryzae koji as an adjunct to prevent rancidity in cheese products.","authors":"Napaporn Chintagavongse, Tomohiro Mitani, Koichi Tamano, Toru Hayakawa, Jun-Ichi Wakamatsu, Haruto Kumura","doi":"10.1093/bbb/zbae174","DOIUrl":"https://doi.org/10.1093/bbb/zbae174","url":null,"abstract":"<p><p>Koji made using Aspergillus oryzae shows potential for application as a cheese adjunct; however, flavor defects resulting from volatile free fatty acid (FFA) accumulation should be avoided. Hence, a modified glucose-containing whey solid medium was used to culture A. oryzae AHU 7139, and the triacylglycerol (TG) lipase activity and lipase gene (tglA and mdlB) expression were compared with those of a culture using a conventional whey solid medium. The results showed that TG lipase activity and the expression of both lipase genes were reduced in the modified medium. Moreover, the expression level of farA, a positive transcription factor of the lipase genes, was also reduced. The cheese adjunct prepared by culturing the AHU 7139 strain in the modified medium lowered the FFA content in the cheese products, resulting in comparable FFA levels with those in the adjunct-free cheese. Thus, adding glucose is recommended to prepare the koji adjunct for cheesemaking.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gene cloning and characterization of N-carbamyl-l-glutamic acid amidohydrolase involved in ergothioneine utilization in Burkholderia sp. HME13.
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-28 DOI: 10.1093/bbb/zbae180
Hisashi Muramatsu, Masaaki Yamada, Hiroki Maguchi, Shin-Ichiro Kato
{"title":"Gene cloning and characterization of N-carbamyl-l-glutamic acid amidohydrolase involved in ergothioneine utilization in Burkholderia sp. HME13.","authors":"Hisashi Muramatsu, Masaaki Yamada, Hiroki Maguchi, Shin-Ichiro Kato","doi":"10.1093/bbb/zbae180","DOIUrl":"https://doi.org/10.1093/bbb/zbae180","url":null,"abstract":"<p><p>Burkholderia sp. HME13 utilizes ergothioneine, a strong antioxidant, as the nitrogen source. We have previously shown that ergothionase (ErtA), thiourocanate hydratase (ErtB), 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase (ErtC), and hydantoin-5-propionic acid amidohydrolase (ErtD) may be involved in ergothioneine utilization in this strain. In this study, we identified the ertE gene in Burkholderia sp. HME13, which encodes a bivalent metal-dependent N-carbamyl-l-glutamic acid amidohydrolase. ErtE showed maximum activity at 60°C and pH 7.0 and was stable at temperatures up to 55°C and pH 6.5-8.0. The Km and Vmax values of ErtE for N-carbamyl-l-glutamic acid were 0.74 mM and 140 U/mg, respectively. EDTA-treated ErtE showed no enzymatic activity, which was restored upon the addition of Co2+, Mn2+, Ni2+, and Fe2+. Expression analyses and enzymatic assays suggested that ErtE is involved in ergothioneine utilization in this strain. Finally, we propose a mechanism for ergothioneine utilization in Burkholderia sp. HME13.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The usefulness of C. elegans life span analysis in screening for functional foods. 在筛选功能性食品过程中利用线虫寿命分析的实用性。
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-26 DOI: 10.1093/bbb/zbae178
Kayo Yasuda
{"title":"The usefulness of C. elegans life span analysis in screening for functional foods.","authors":"Kayo Yasuda","doi":"10.1093/bbb/zbae178","DOIUrl":"https://doi.org/10.1093/bbb/zbae178","url":null,"abstract":"<p><p>Caenorhabditis elegans is a type of nematode that has significantly contributed to aging research as a multicellular animal model because of its high reproductive rate, ease of cultivation, low cost, short generation cycle, body transparency, and eukaryotic nature. Since the discovery of long-lived mutant strains of C. elegans, signaling pathways involved in lifespan have been elucidated. Some of these pathways are shared with mammals, indicating that aging research in C. elegans may be applied to other animals, including humans. Studies on the mechanisms of aging have advanced with the availability of mutants for these pathways. In recent years, C. elegans has also contributed to the discovery of antioxidants and the elucidation of the molecular mechanisms responsible for the anti-aging effects of foods and traditional medicines with lifespan as an indicator. This review summarizes the characteristics of C. elegans for life span analysis associated with functional foods.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142726202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of lignin on indigo-reducing activity and indigo particle size in indigo dye suspensions. 木质素对靛蓝染料悬浮液中靛蓝还原活性和靛蓝粒径的影响
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-26 DOI: 10.1093/bbb/zbae151
Kasumi Nakagawa, Haruka Ohata, Michiki Takeuchi, Momoka Matsunaga, Keisei Sowa, Takaiku Sakamoto, Akinori Ando, Chikako Asada, Jun Ogawa, Kenji Kano, Eiji Sakuradani
{"title":"Effects of lignin on indigo-reducing activity and indigo particle size in indigo dye suspensions.","authors":"Kasumi Nakagawa, Haruka Ohata, Michiki Takeuchi, Momoka Matsunaga, Keisei Sowa, Takaiku Sakamoto, Akinori Ando, Chikako Asada, Jun Ogawa, Kenji Kano, Eiji Sakuradani","doi":"10.1093/bbb/zbae151","DOIUrl":"https://doi.org/10.1093/bbb/zbae151","url":null,"abstract":"<p><p>Microbial indigo reduction is a key reaction in indigo dyeing; however, the mechanism of the interaction with indigo remains unclear. We hypothesized that lignin is a candidate substance that supports this interaction. The addition of lignin effectively enhanced the indigo reduction. The reducing activity of indigo correlated with the particle size after the addition of lignin.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Physiology of vitamin B12: a study on its molecular mechanisms using a Caenorhabditis elegans model. 维生素 B12 的生理学：利用秀丽隐杆线虫模型对其分子机制的研究。
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-25 DOI: 10.1093/bbb/zbae169
Tomohiro Bito
{"title":"Physiology of vitamin B12: a study on its molecular mechanisms using a Caenorhabditis elegans model.","authors":"Tomohiro Bito","doi":"10.1093/bbb/zbae169","DOIUrl":"https://doi.org/10.1093/bbb/zbae169","url":null,"abstract":"<p><p>Vitamin B12 (B12) is a water-soluble substance that is a member of the B-vitamin family. Its recommended daily dose in adult men and women is 2.4 µg, which is the lowest among the 13 vitamins. B12 deficiency causes megaloblastic anemia and neurological disorders. It is also associated with cognitive decline, growth retardation, infertility, and other symptoms. Nevertheless, the detailed mechanisms of which remain unclear. Caenorhabditis elegans is a small organism, with a length of approximately 1 mm and a lifespan of approximately 3 weeks. It has similar fundamental biological structures, such as the muscles, nervous system, and digestive tract, with mammals. Previous studies have shown that B12 is required for the normal development of C. elegans, similar to that of mammals. The current study aimed to perform a detailed investigation of the mechanisms underlying the development of B12 deficiency using a dietary B12-deficient C. elegans model.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptome analysis reveals selectively high expression of beige adipocyte marker genes in mouse perinephric fat. 转录组分析揭示了小鼠肾周脂肪中米色脂肪细胞标记基因的选择性高表达。
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-22 DOI: 10.1093/bbb/zbae143
Yoshinori Misawa, Yu Takahashi, Takashi Sasaki, Ryuichiro Sato, Yoshio Yamauchi
{"title":"Transcriptome analysis reveals selectively high expression of beige adipocyte marker genes in mouse perinephric fat.","authors":"Yoshinori Misawa, Yu Takahashi, Takashi Sasaki, Ryuichiro Sato, Yoshio Yamauchi","doi":"10.1093/bbb/zbae143","DOIUrl":"10.1093/bbb/zbae143","url":null,"abstract":"<p><p>To reveal the differences in the properties of visceral adipose tissue in healthy unstimulated mice, we performed transcriptome analysis using RNA sequencing. Among visceral adipose tissues, perinephric adipose tissue was found to exclusively express beige adipocyte markers while expressing white adipocyte markers. These results imply potential specific roles of perinephric adipose tissue in both physiological and pathological conditions.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1449-1452"},"PeriodicalIF":1.4,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142458179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synergistic effect of cerium chloride and calcium chloride alters calcium signaling in keratinocytes to promote epidermal differentiation. 氯化铈和氯化钙的协同效应可改变角质形成细胞中的钙信号转导，促进表皮分化。
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-22 DOI: 10.1093/bbb/zbae131
Kei Tsukui, Masamitsu Suzuki, Miyu Amma, Yoshihiro Tokudome
{"title":"Synergistic effect of cerium chloride and calcium chloride alters calcium signaling in keratinocytes to promote epidermal differentiation.","authors":"Kei Tsukui, Masamitsu Suzuki, Miyu Amma, Yoshihiro Tokudome","doi":"10.1093/bbb/zbae131","DOIUrl":"10.1093/bbb/zbae131","url":null,"abstract":"<p><p>Epidermal keratinocytes undergo morphological and functional changes during differentiation, eventually being enucleated to become corneocytes. Calcium has been shown to be involved in various cellular functions of epidermal cells, including proliferation, differentiation, and apoptosis. Cerium is a lanthanide-series element and rare earth metal. For skin, cerium oxide has been investigated for use in absorbing UV and promoting wound healing. However, the functions and physiological effects of inorganic cerium on the skin have rarely been investigated. Here, we focused on cerium's function in epidermal keratinocytes and its interaction with calcium by investigating their effects on cell differentiation and intracellular calcium concentration. This study showed that applying cerium chloride to epidermal keratinocytes altered calcium signaling. It also suggested that cerium and calcium induced an increase in intracellular calcium concentration and promoted keratinocyte differentiation.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1432-1441"},"PeriodicalIF":1.4,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142341805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Expression patterns of Arabidopsis thaliana RecQ-like (AtRecQl) genes and the roles of AtRecQl2 and AtRecQl3 in response to abiotic stress. 拟南芥 RecQ 样基因（AtRecQl）的表达模式以及 AtRecQl2 和 AtRecQl3 在应对非生物胁迫中的作用。
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-22 DOI: 10.1093/bbb/zbae136
Amit Kumar Dutta, Md Firose Hossain, Mst Momtaz Sultana, Takushi Hachiya, Tsuyoshi Nakagawa
{"title":"Expression patterns of Arabidopsis thaliana RecQ-like (AtRecQl) genes and the roles of AtRecQl2 and AtRecQl3 in response to abiotic stress.","authors":"Amit Kumar Dutta, Md Firose Hossain, Mst Momtaz Sultana, Takushi Hachiya, Tsuyoshi Nakagawa","doi":"10.1093/bbb/zbae136","DOIUrl":"10.1093/bbb/zbae136","url":null,"abstract":"<p><p>Helicases are involved in almost every nucleic acid metabolism process. Within this family, RecQ helicase proteins protect genome integrity across all organisms through DNA recombination, repair, and replication. This study focused on five Arabidopsis thaliana RecQ-like (AtRecQl) genes with diverse functionalities. Analysis of ProAtRecQl: GUS expression during vegetative and reproductive development stages revealed organ- and tissue-specific patterns. Changes in AtRecQls transcript levels in response to abiotic stressors suggest their involvement in diverse stimuli responses. Notably, germination and growth rates were lower in atrecql2 and atrecql3 mutants under various salt concentrations and cold conditions. These findings indicate that AtRecQl2 and AtRecQl3 act as positive regulators of abiotic stress tolerance during the germinative and postgerminative phases.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1411-1423"},"PeriodicalIF":1.4,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142341801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Carnosic acid inhibits integrin expression and prevents pulmonary metastasis of melanoma. 肉苁蓉能抑制整合素的表达并防止黑色素瘤的肺转移。
IF 1.4 4区 生物学
Bioscience, Biotechnology, and Biochemistry Pub Date : 2024-11-22 DOI: 10.1093/bbb/zbae177
Sachi Shibata, Kohei Yamada, Shigeyuki Kon
{"title":"Carnosic acid inhibits integrin expression and prevents pulmonary metastasis of melanoma.","authors":"Sachi Shibata, Kohei Yamada, Shigeyuki Kon","doi":"10.1093/bbb/zbae177","DOIUrl":"https://doi.org/10.1093/bbb/zbae177","url":null,"abstract":"<p><p>Carnosic acid is a naturally occurring, plant-derived polyphenolic abietane diterpene with anti-tumor properties. However, its underlying mechanisms are still unclear. Therefore, we investigated the effects of carnosic acid on lung metastasis in a murine melanoma model. C57BL/6 mice were intravenously injected with B16-BL6 cells, followed by carnosic acid treatment. Lung weights were recorded, and tumor cell colonies were counted at the end of the experiment. Integrin expression was evaluated using flow cytometry and cell adhesion assays. Lung weights were significantly lower in the carnosic acid group than in the control group, indicating the suppression of metastasis. Carnosic acid suppressed α4 integrin expression in B16-BL6 cells and inhibited α4 and α9 integrin-dependent cell adhesion. Thus, our data suggest that carnosic acid prevents lung metastasis, possibly by suppressing integrin expression. Our findings support the clinical application of carnosic acid as a potential natural anti-tumor agent, offering a complementary approach to conventional therapies.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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