{"title":"The effect of the formalin-fixed paraffin-embedded process on salivary microbiota profiling.","authors":"Hiroto Sano, Takuichi Sato, Yoriaki Kanri, Junya Ono, Yasuo Okada","doi":"10.2220/biomedres.44.117","DOIUrl":"https://doi.org/10.2220/biomedres.44.117","url":null,"abstract":"<p><p>In recent years, bacterial DNA in formalin-fixed paraffin-embedded (FFPE) samples has been recognized as a valuable bioresource for microbiota studies. This study aimed to examine the effect of the FFPE process on microbiota profiling to evaluate whether FFPE samples could serve as an alternative bioresource to fresh samples in oral microbiota studies. Fresh saliva was collected from nine subjects. The pellets obtained by centrifuging the collected saliva were fixed in formalin, then dehydrated and embedded in paraffin to prepare FFPE samples. The abundance of the hypervariable regions V1-9, V1-2, and V3-4 of the 16S rRNA gene in fresh and FFPE samples was relatively compared. In addition, microbiota profiling was performed to compare the results between the two sample types. The results showed that the FFPE process resulted in a certain degree of fragmentation of the 16S rRNA gene. However, the V1-2 region was relatively well-preserved compared to the V1-9 and V3-4 regions, suggesting that short regions are suitable targets for oral microbiota analysis. Importantly, there were no significant differences in alpha and beta diversity of microbiota between fresh and FFPE samples, and microbiota profiles were similar between the two sample types, suggesting that FFPE samples could be a valuable bioresource for oral microbiota studies.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9565502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Impact of somatic mutations and transcriptomic alterations on cancer aneuploidy.","authors":"Keiichi Hatakeyama, Takeshi Nagashima, Keiichi Ohshima, Sumiko Ohnami, Shumpei Ohnami, Yuji Shimoda, Akane Naruoka, Koji Maruyama, Akira Iizuka, Tadashi Ashizawa, Hirotsugu Kenmotsu, Tohru Mochizuki, Kenichi Urakami, Yasuto Akiyama, Ken Yamaguchi","doi":"10.2220/biomedres.44.187","DOIUrl":"10.2220/biomedres.44.187","url":null,"abstract":"<p><p>Aneuploidy has been recognized as one of hallmark of tumorigenesis since the early 20th century. Recent developments in structural variation analysis in the human genome have revealed the diversity of aneuploidy in cancer. However, the effects of gene mutation and expression in tumors on aneuploidy remain poorly understood. Here, we performed whole exome analysis of over 5,000 Japanese cancer cases and investigated the impact of somatic mutations and gene expression alterations on aneuploidy. First, we evaluated tumor content and genomic alterations that could influence aneuploidy. Next, we compared the aneuploidy frequency in 18 cancer types and observed that TP53 mutations were associated with the aneuploidy on specific chromosomes in colorectal and gastric cancers. Finally, we used expression analysis to isolate pathways involved in aneuploidy accumulation from tumors without TP53 mutations. Chromosomal instability and cell cycle aberration were associated with aneuploidy in TP53 wild-type tumors, and 26 commonly upregulated genes were identified in aneuploidy-high solid tumors without TP53 mutations. Among them, two cancer-related genes (CENPA and PBK) were involved in aneuploidy. Our integrated analysis revealed that both TP53 mutations and transcriptomic alterations independent of somatic mutations affect aneuploidy accumulation. Our findings will facilitate further understanding of diverse aneuploidies in the tumorigenesis.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41094146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"3-Iodothyronamine, a trace amine-associated receptor agonist, regulates intracellular Ca2+ increases via CaMK II through Epac2 in rat cerebral arterioles.","authors":"Wakana Sakanoue, Takuya Yokoyama, Masato Hirakawa, Satsuki Maesawa, Kenichi Sato, Tomoyuki Saino","doi":"10.2220/biomedres.44.219","DOIUrl":"10.2220/biomedres.44.219","url":null,"abstract":"<p><p>Trace amines (TAs) in the nervous system bind to TA-associated receptors (TAARs) and are involved in the regulation of monoaminergic functions. Among TAAR subtypes, TAAR1 has been implicated in the development of neurological disorders, such as schizophrenia. The present study investigated the effects of the TAAR1 agonist, 3-iodothyronamine (T1AM) on cerebral arterioles using fluctuations in the intracellular concentration of Ca2+ ([Ca2+]i) as an index of contractile responses. In cerebral arterioles, most of the TAAR agonists did not increase [Ca2+]i, while only T1AM elevated [Ca2+]i in vascular smooth muscle cells. This increase involved extracellular Ca2+ influx through T-type Ca2+ channels and inositol trisphosphate- and ryanodine-receptor-mediated Ca2+ release from intracellular stores. The inhibition of the cAMP sensor, exchange protein directly activated by cAMP (Epac) 2, and calmodulin kinase (CaMK) II strongly inhibited Ca2+ elevations. The present study revealed that T1AM acted not only on the TAAR1 receptor as previously suggested, but also on other G-protein coupled receptors and/or signal transduction systems to increase intracellular Ca2+ in cerebral arteriole smooth muscle cells. These results suggest that when using T1AM in clinical practice, attention should be paid to the early rise in blood pressure.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41153890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"IL-33 deficiency suppresses alveolar bone loss in a ligature-induced periodontitis model.","authors":"Natsuko Aida, Kazuyoshi Takeda, Susumu Nakae, Hirohisa Saito, Ko Okumura, Toshifumi Azuma, Tatsukuni Ohno","doi":"10.2220/biomedres.44.9","DOIUrl":"https://doi.org/10.2220/biomedres.44.9","url":null,"abstract":"<p><p>Interleukin-33 (IL-33) is a member of the IL-1 cytokine family that has been studied primarily in the context of type 2 immune responses. Recent reports suggest that IL-33 also enhances the func- tions of various immune cells and contributes to the development of different inflammatory diseas- es. Interestingly, IL-33 and its receptor ST2 axis exerted either inhibitory or promotional effects on alveolar bone loss in various periodontitis models. Using a mouse model of ligature-induced periodontitis, we found that the levels of mRNAs encoding IL-33 and other inflammatory cyto- kines (IL-1α, IL-1β, IL-6, and TNFα) were augmented in gingival tissues of wild-type (WT) mice, and that the alveolar bone loss amount was lower in IL-33-deficient than WT mice. The numbers and proportions of IFN-γ-producing CD8+ T and regulatory T cells were decreased while those of Th17 cells were increased in the draining lymph nodes of IL-33-deficient mice compared to WT mice. Additionally, the level of RNA encoding an osteoclastogenic molecule, i.e., receptor activa- tor of nuclear factor kappa-B ligand (RANKL), in ligated gingival tissue was higher in IL-33-defi- cient than WT mice. These results suggest that IL-33 is involved in alveolar bone loss in the ligature-induced periodontitis model, although IL-33 may inhibit osteoclast differentiation.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9145539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Acute effect of electrical stimulation on muscle protein synthesis and break-down in the soleus muscle of hindlimb unloaded rats.","authors":"Miho Kanazashi, Masayuki Tanaka","doi":"10.2220/biomedres.44.209","DOIUrl":"https://doi.org/10.2220/biomedres.44.209","url":null,"abstract":"<p><p>Electrical stimulation (ES) is effective for disuse-induced muscle atrophy. However, the acute effect of ES on muscle protein synthesis (MPS) and muscle protein breakdown (MPB) remains unclear. We investigated the effect of a single-session ES treatment on mTORC1 signaling, MPS, and MPB in the soleus muscle of 2-week hindlimb unloaded rats. Sprague Dawley rats (n = 12 male) were randomly divided into control (CON) and hindlimb unloaded (HU) groups. After 2 weeks, the right soleus muscle was percutaneously stimulated and underwent supramaximal isometric contractions. The left soleus muscle served as an internal control. We collected soleus muscle samples 6 h after ES. Two weeks of HU decreased p70S6K and S6rp activation, downstream factors for mTORC1 signaling, and SUnSET method-assessed MPS, but increased the LC3-II/I ratio, an indicator of autophagy. ES on disused muscle successfully activated mTORC1 signaling but did not affect MPS. Contrary, ES decreased ubiquitinated proteins expression and LC3B-II/I ratio. HU might affect mTORC1 activation and MPS differently in response to acute ES possibly due to excessive ROS production caused by ES. Our findings suggest that ES applied to disused skeletal muscles may suppress MPB, but its effect on MPS appears to be attenuated.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41106020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Hypoxia-induced endothelial cell-derived exosome stimulates vascular smooth muscle cell proliferation and migration.","authors":"Qinggen Xiong, Fei Lu, Xiaoming Xie, Wei Zhou","doi":"10.2220/biomedres.44.245","DOIUrl":"10.2220/biomedres.44.245","url":null,"abstract":"<p><p>This study mainly used human VSMCs and ECs cultured in vitro to investigate whether exosomes (Exos) are involved in the communication between ECs and VSMCs under hypoxia, and to explore the role and mechanism of ECs-derived exosomes in the abnormal proliferation of VSMCs. VSMCs proliferation and migration were assessed by a series of cell function assays after culturing VSMCs alone or co-culturing ECs under hypoxia or normoxia. Next, exosomes were extracted from ECs under hypoxia or normoxia and characterized. We then introduced ECs-Exos to observe their effects on VSMCs proliferation and migration, and further evaluated the expression of transforming growth factor-beta receptor 1 (TGFBR1) pathway-related proteins. Finally, the effect of ECs-Exos on VSMCs function was evaluated after knocking down TGFBR1 in ECs. VSMCs treated with ECs-Exos exhibited increased proliferation and migration ability in hypoxic environment, and the expression of TGFBR1 pathway-related proteins was upregulated. Administration of ECs-Exos with TGFβ1 knockdown conspicuously reversed the promoting effects of ECs-Exos on cell proliferation and migration under hypoxia. In summary, hypoxia affected the secretion of extracellular vesicles by endothelial cells, which can be internalized by VSMCs and accelerate the abnormal proliferation and migration of VSMCs by delivering TGFBR1.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138440302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Allergic inflammation disrupts epithelial electrogenic electrolyte transport through cholinergic regulation in the mouse colon.","authors":"Takeshi Yamamoto, Yosuke Katsuki, Yuya Kanauchi, Shusaku Hayashi, Makoto Kadowaki","doi":"10.2220/biomedres.44.31","DOIUrl":"https://doi.org/10.2220/biomedres.44.31","url":null,"abstract":"<p><p>Intestinal transport of electrolytes is regulated by the enteric nervous system. Acetylcholine (ACh) is considered the most important neurotransmitter for electrolyte transport in the colon. However, electrolyte transport regulated by ACh is not fully understood in the colon. We investigated the regulation of electrogenic electrolyte transport by cholinergic agonists in the mouse colon by measuring the short-circuit current (Isc) using an Ussing chamber system. Muscarinic stimulation induced transient electrogenic Cl- secretion, and nicotinic stimulation induced electrogenic K+ secretion to the apical side in the normal mouse colon, and these effects were reduced in the colon of mice with food allergy (FA). Administration of prednisolone to mice with FA suppressed mild inflammation in the colon and allergic symptoms and thereby ameliorated the disruption of electrogenic electrolyte transport induced not only by cholinergic pathway activation but also by electrical field stimulation and intracellular cAMP signaling pathway activation in the colon. These results suggest that the electrogenic electrolyte transport function in the colon is impaired by FA-induced colonic inflammation and that the suppression of inflammation ameliorates the dysfunction of electrogenic electrolyte transport in the colon of mice with FA.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9145537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Neonatal bilateral whisker trimming in male mice age-dependently alters brain neurotransmitter levels and causes adolescent onsets of social behavior abnormalities.","authors":"Hiroyasu Murasawa, Hitomi Soumiya, Hiroyuki Kobayashi, Jun Imai, Takahiko Nagase, Hidefumi Fukumitsu","doi":"10.2220/biomedres.44.147","DOIUrl":"https://doi.org/10.2220/biomedres.44.147","url":null,"abstract":"<p><p>Tactile perception via whiskers is important in rodent behavior. Whisker trimming during the neonatal period affects mouse behaviors related to both whisker-based tactile cognition and social performance. However, the molecular basis of these phenomena is not completely understood. To solve this issue, we investigated developmental changes in transmitters and metabolites in various brain regions of male mice subjected to bilateral whisker trimming during the neonatal period (10 days after birth [BWT10 mice]). We discovered significantly lower levels of 3-methoxy-4-hydroxyphenyl glycol (MHPG), the major noradrenaline metabolite, in various brain regions of male BWT10 mice at both early/late adolescent stages (at P4W and P8W). However, reduced levels of dopamine (DA) and their metabolites were more significantly identified at P8W in the nuclear origins of monoamine (midbrain and medulla oblongata) and the limbic system (frontal cortex, amygdala, and hippocampus) than at P4W. Furthermore, the onset of social behavior deficits (P6W) was observed later to the impairment of whisker-based tactile cognitive behaviors (P4W). Taken together, these findings suggest that whisker-mediated tactile cognition may contribute toprogressive abnormalities in social behaviors in BWT10 mice accompanied by impaired development of dopaminergic systems.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9943307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasuyuki Sasano, Alu Konno, Megumi Nakamura, Akiko Henmi, Miyuki Mayanagi, Mu-Chen Yang, Ikuko Yao
{"title":"Visualization of the localization of phospholipids in developing rat teeth by matrix-assisted laser desorption/ionization imaging mass spectrometry.","authors":"Yasuyuki Sasano, Alu Konno, Megumi Nakamura, Akiko Henmi, Miyuki Mayanagi, Mu-Chen Yang, Ikuko Yao","doi":"10.2220/biomedres.44.173","DOIUrl":"https://doi.org/10.2220/biomedres.44.173","url":null,"abstract":"<p><p>Matrix-assisted laser desorption/ionization imaging mass spectrometry (IMS) is used to comprehensively visualize the spatial distribution of numerous biomolecules. The present study was designed to investigate the distribution of phospholipids in developing rat teeth by IMS to identify the characteristic phospholipid molecules for tooth development, and to evaluate the suitability of tissue preparation methods. Rats at postnatal day 3 were euthanized, and the resected head specimens were either fixed or not fixed with 4% paraformaldehyde (PFA), and decalcified or not decalcified in 10% ethylenediaminetetraacetic acid (EDTA) before being frozen. Subsequently, sections were prepared and mounted on glass slides coated with indium tin oxide, and analyzed by IMS. The mass spectra showed the highest peaks around m/z 706, 732, and 734 in the region of interest. Characteristic localization of signals in the tooth buds was seen around m/z 706 and 732, and a database search indicated that the corresponding molecules were phosphatidylcholines. The signals were localized to the dental papillae and enamel epithelia in the tooth buds. The PFA-fixed specimens with or without EDTA decalcification showed preserved IMS signals, while the non-fixed specimens showed fewer signals. Thus, PFA fixation with EDTA decalcification appears to be suitable for IMS analysis of calcified tissues.</p>","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9943309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Validation of mitotic harvesting method with human cervical carcinoma HeLa cells expressing fluorescent ubiquitination-based cell cycle indicators for radiation research.","authors":"Ryosuke Seino, Hiroto Uno, Hisanori Fukunaga","doi":"10.2220/biomedres.44.181","DOIUrl":"10.2220/biomedres.44.181","url":null,"abstract":"The cell cycle is a series of events in the process of one cell giving rise to two daughter cells. The mitotic harvesting method, established by Terasima and Tolmach in the 1960s, causes minimal physiological stress on the cells and achieves a high degree of cell cycle synchrony by collecting only mitotic cells from a cultured cell system. The purpose of the present study is to validate the versatility of the mitotic harvesting method using human cervical cell line HeLa cells expressing Fluorescent Ubiquitination-based Cell Cycle Indicators (FUCCI) and to estimate the cell cycle-dependent changes in radiosensitivity in HeLa-FUCCI cells. The image analysis showed that cell cycle synchrony was maintained for at least 24 hours after mitotic cell collection. Also, the clonogenic assay demonstrated changes in radiosensitivity that were cell cycle dependent. These results indicate that the mitotic harvesting method using FUCCI-expressing cells has high versatility in the field of radiation cell biology.","PeriodicalId":9138,"journal":{"name":"Biomedical Research-tokyo","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41106680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}