Image-based quantitative determination of DNA damage signal reveals a threshold for G2 checkpoint activation in response to ionizing radiation

Background: Proteins involved in the DNA damage response accumulate as microscopically-visible nuclear foci on the chromatin flanking DNA double-strand breaks (DSBs). As growth of ionizing radiation (IR)-induced foci amplifies the ATM-dependent DNA damage signal, the formation of discrete foci plays a crucial role in cell cycle checkpoint activation, especially in cells exposed to lower doses of IR. However, there is no quantitative parameter for the foci which considers both the number and their size. Therefore, we have developed a novel parameter for DNA damage signal based on the image analysis of the foci and quantified the amount of the signal sufficient for G2 arrest.Results: The parameter that we have developed here was designated as SOID. SOID is an abbreviation of Sum Of Integrated Density, which represents the sum of fluorescence of each focus within one nucleus. The SOID was calculated for individual nucleus as the sum of (area (total pixel numbers) of each focus) x (mean fluorescence intensity per pixel of each focus). Therefore, the SOID accounts for the number, size, and fluorescence density of IR-induced foci, and the parameter reflects the flux of DNA damage signal much more accurately than foci number. Using very low doses of X-rays, we performed a "two-way" comparison of SOID of Ser139-phosphorylated histone H2AX foci between G2-arrested cells and mitosis-progressing cells, and between mitosis-progressing cells in the presence or absence of ATM or Chk1/2 inhibitor, both of which abrogate IR-induced G2/M checkpoint. The analysis revealed that there was a threshold of DNA damage signal for G2 arrest, which was around 4000~5000 SOID. G2 cells with < 4000 SOID were neglected by G2/M checkpoint, and thus, the cells could progress to mitosis. Chromosome analysis revealed that the checkpoint-neglected and mitosis-progressing cells had approximately two chromatid breaks on average, indicating that 4000~5000 SOID was equivalent to a few DNA double strand breaks.Conclusions: We developed a novel parameter for quantitative analysis of DNA damage signal, and we determined the threshold of DNA damage signal for IR-induced G2 arrest, which was represented by 4000~5000 SOID. The present study emphasizes that not only the foci number but also the size of the foci must be taken into consideration for the proper quantification of DNA damage signal

酢酸摂取と運動が脂肪代謝と運動耐久性に及ぼす影響

Previously, we found that acetic acid had effects on lipid metabolism in skeletal muscles and has functions that work against obesity and obesity-linked type 2 diabetes through the activation of AMPactivated protein kinase (AMPK). During exercise, AMPK is activated in skeletal muscle according to exercise intensity and it increases fatty acid oxidation. The purpose of this study was to investigate the interactive effects of chronic intake of acetic acid and exercise training on lipid metabolism and endurance performance. Six-week-old SD rats were randomly assigned to four groups: water-injected (rest-water), acetic acid-injected (rest-ace), exercise-trained after injection of water (water-ex), and exercise-trained after injection of acetic acid (ace-ex) for 4 weeks. Body weight (BW) in rest-ace and ace-ex groups was significantly lower than rest-water group. Exercise-training groups showed an increase of exercise capacity, by the addition of intake of acetic acid, lipid oxidation was promoted during exercise tolerance test. Skeletal muscle of rats treated with acetic acid and exercise training led to higher expressions of cytochrome c (cycs), and tended to stimulate expressions of peroxisome proliferator-activated receptor coactivator 1-α (PGC1-α ) and MHC1 genes than those of rest-water group. Those results indicate that treatments both of exercise training and intake of acetic acid contribute to enhancement of lipid metabolism and improvement of exercise capacity.これまで我々は、酢酸の摂取が骨格筋内のAMP活性化プロテインキナーゼ（AMPK）の活性化を介して脂質代謝と肥満、肥満に関連した2型糖尿病の予防に効果があることを示唆してきた。AMPKは運動によって骨格筋で活性化し、脂肪酸酸化を促進する。この研究は、4週間の継続的な酢酸摂取と運動トレーニングが運動中の脂肪代謝と運動耐久性に及ぼす影響について調べることを目的とした。　6週齢のSD系雄ラットを安静期に水を摂取するrest-water群、酢酸を摂取するrest-ace群、運動前に水を摂取するwater-ex群、運動前に酢酸を摂取するace-ex群に無作為に分け実験を行った。酢酸を継続的に摂取すると水摂取に比較して腹腔内脂肪量の減少と体重増加の抑制がみられた。また継続的な酢酸摂取および運動トレーニングにより、耐久性運動下でのグルコース利用の抑制および脂肪酸酸化の促進が見られた。酢酸摂取および運動トレーニング群の腓腹筋では、MHCIおよびcytochrome c等の遅筋線維マーカー遺伝子が増加していた。継続的な酢酸摂取と運動トレーニングにより、脂肪代謝と運動耐久性の向上が示唆された

Distribution of Japanese Eel Anguilla japonica Revealed by Environmental DNA

絶滅危惧種ニホンウナギの分布域を環境DNA解析で推定. 京都大学プレスリリース. 2021-03-03.The abundance of Japanese eel Anguilla japonica has rapidly decreased in recent decades. Following a re-evaluation of the possibility of extinction, the Japanese Ministry of the Environment and the International Union for Conservation of Nature listed the Japanese eel as an endangered species in 2013 and 2014, respectively. However, their abundance and precise distribution have never been clarified owing to their nocturnality and difficulty in their capture. In this study, the distribution of Japanese eels was investigated by monitoring for environmental DNA (eDNA), a non-invasive and efficient detection method. A total of 365 water samples were collected from 265 rivers located throughout Japan. High concentrations of eDNA of Japanese eels were detected in rivers on the Pacific side, but were low in the Sea of Japan side. In particular, very little eDNA amplification was confirmed from Hokkaido and the north of the Sea of Japan. The eDNA distribution in Japanese rivers coincides with the transport of the larvae in the ocean, as estimated by numerical simulations. Generalized linear mixed models were developed to explain the distribution of eDNA concentrations. The total nitrogen concentration emerged as an important factor in the best model. These results indicate that the distribution of Japanese eel is mostly determined by the maritime larval transport, and their survival and growth depend on the abundance of food in the river. The findings of the present study are useful for the management of populations and in the conservation of Japanese eels

β5t shapes CD8 T cells without negative selection

The thymoproteasome expressed specifically in thymic cortical epithelium optimizes the generation of CD8+ T cells; however, how the thymoproteasome contributes to CD8+ T cell development is unclear. Here, we show that the thymoproteasome shapes the TCR repertoire directly in cortical thymocytes before migration to the thymic medulla. We further show that the thymoproteasome optimizes CD8+ T cell production independent of the thymic medulla; independent of additional antigen-presenting cells, including medullary thymic epithelial cells and dendritic cells; and independent of apoptosis-mediated negative selection. These results indicate that the thymoproteasome hardwires the TCR repertoire of CD8+ T cells with cortical positive selection independent of negative selection in the thymus

Synthesis and pharmacological characterization of potent, selective, and orally bioavailable isoindoline class dipeptidyl peptidase IV inhibitors

Focused structure-activity relationships of isoindoline class DPP-IV inhibitors have led to the discovery of 4b as a highly selective, potent inhibitor of DPP-IV. In vivo studies in Wistar/ST rats showed that 4b was converted into the strongly active metabolite 4l in high yield, resulting in good in vivo efficacy for antihyperglycemic activity

Generation of Tetrafluoroethylene–Propylene Elastomer-Based Microfluidic Devices for Drug Toxicity and Metabolism Studies

フッ素系エラストマー素材を用いた肝臓チップの開発と薬物代謝・毒性試験への応用. 京都大学プレスリリース. 2021-09-16.Drug testing on miniatured livers. 京都大学プレスリリース. 2021-09-17.Polydimethylsiloxane (PDMS) is widely used to fabricate microfluidic organs-on-chips. Using these devices (PDMS-based devices), the mechanical microenvironment of living tissues, such as pulmonary respiration and intestinal peristalsis, can be reproduced in vitro. However, the use of PDMS-based devices in drug discovery research is limited because of their extensive absorption of drugs. In this study, we investigated the feasibility of the tetrafluoroethylene–propylene (FEPM) elastomer to fabricate a hepatocyte-on-a-chip (FEPM-based hepatocyte chip) with lower drug absorption. The FEPM-based hepatocyte chip expressed drug-metabolizing enzymes, drug-conjugating enzymes, and drug transporters. Also, it could produce human albumin. Although the metabolites of midazolam and bufuralol were hardly detected in the PDMS-based hepatocyte chip, they were detected abundantly in the FEPM-based hepatocyte chip. Finally, coumarin-induced hepatocyte cytotoxicity was less severe in the PDMS-based hepatocyte chip than in the FEPM-based hepatocyte chip, reflecting the different drug absorptions of the two chips. In conclusion, the FEPM-based hepatocyte chip could be a useful tool in drug discovery research, including drug metabolism and toxicity studies