Mitochondria and G-quadruplex evolution: an intertwined relationship

G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes

Upscaling Wetland Methane Emissions From the FLUXNET-CH4 Eddy Covariance Network (UpCH4 v1.0):Model Development, Network Assessment, and Budget Comparison

Wetlands are responsible for 20%–31% of global methane (CH4) emissions and account for a large source of uncertainty in the global CH4 budget. Data-driven upscaling of CH4 fluxes from eddy covariance measurements can provide new and independent bottom-up estimates of wetland CH4 emissions. Here, we develop a six-predictor random forest upscaling model (UpCH4), trained on 119 site-years of eddy covariance CH4 flux data from 43 freshwater wetland sites in the FLUXNET-CH4 Community Product. Network patterns in site-level annual means and mean seasonal cycles of CH4 fluxes were reproduced accurately in tundra, boreal, and temperate regions (Nash-Sutcliffe Efficiency ∼0.52–0.63 and 0.53). UpCH4 estimated annual global wetland CH4 emissions of 146 ± 43 TgCH4 y−1 for 2001–2018 which agrees closely with current bottom-up land surface models (102–181 TgCH4 y−1) and overlaps with top-down atmospheric inversion models (155–200 TgCH4 y−1). However, UpCH4 diverged from both types of models in the spatial pattern and seasonal dynamics of tropical wetland emissions. We conclude that upscaling of eddy covariance CH4 fluxes has the potential to produce realistic extra-tropical wetland CH4 emissions estimates which will improve with more flux data. To reduce uncertainty in upscaled estimates, researchers could prioritize new wetland flux sites along humid-to-arid tropical climate gradients, from major rainforest basins (Congo, Amazon, and SE Asia), into monsoon (Bangladesh and India) and savannah regions (African Sahel) and be paired with improved knowledge of wetland extent seasonal dynamics in these regions. The monthly wetland methane products gridded at 0.25° from UpCH4 are available via ORNL DAAC (https://doi.org/10.3334/ORNLDAAC/2253).</p

Upscaling Wetland Methane Emissions From the FLUXNET-CH4 Eddy Covariance Network (UpCH4 v1.0): Model Development, Network Assessment, and Budget Comparison

Wetlands are responsible for 20%-31% of global methane (CH4) emissions and account for a large source of uncertainty in the global CH4 budget. Data-driven upscaling of CH4 fluxes from eddy covariance measurements can provide new and independent bottom-up estimates of wetland CH4 emissions. Here, we develop a six-predictor random forest upscaling model (UpCH4), trained on 119 site-years of eddy covariance CH4 flux data from 43 freshwater wetland sites in the FLUXNET-CH4 Community Product. Network patterns in site-level annual means and mean seasonal cycles of CH4 fluxes were reproduced accurately in tundra, boreal, and temperate regions (Nash-Sutcliffe Efficiency similar to 0.52-0.63 and 0.53). UpCH(4) estimated annual global wetland CH4 emissions of 146 +/- 43 TgCH4 y(-1) for 2001-2018 which agrees closely with current bottom-up land surface models (102-181 TgCH4 y(-1)) and overlaps with top-down atmospheric inversion models (155-200 TgCH4 y -1). However, UpCH4 diverged from both types of models in the spatial pattern and seasonal dynamics of tropical wetland emissions. We conclude that upscaling of eddy covariance CH4 fluxes has the potential to produce realistic extra-tropical wetland CH4 emissions estimates which will improve with more flux data. To reduce uncertainty in upscaled estimates, researchers could prioritize new wetland flux sites along humid-to-arid tropical climate gradients, from major rainforest basins (Congo, Amazon, and SE Asia), into monsoon (Bangladesh and India) and savannah regions (African Sahel) and be paired with improved knowledge of wetland extent seasonal dynamics in these regions. The monthly wetland methane products gridded at 0.25 degrees from UpCH4 are available via ORNL DAAC (https://doi.org/10.3334/ ORNLDAAC/2253).Plain Language Summary Wetlands account for a large share of global methane emissions to the atmosphere, but current estimates vary widely in magnitude (similar to 30% uncertainty on annual global emissions) and spatial distribution, with diverging predictions for tropical rice growing (e.g., Bengal basin), rainforest (e.g., Amazon basin), and floodplain savannah (e.g., Sudd) regions. Wetland methane model estimates could be improved by increased use of land surface methane flux data. Upscaling approaches use flux data collected across globally distributed measurement networks in a machine learning framework to extrapolate fluxes in space and time. Here, we train and evaluate a methane upscaling model (UpCH4) and use it to generate monthly, globally gridded wetland methane emissions estimates for 2001-2018. The UpCH4 model uses only six predictor variables among which temperature is dominant. Global annual methane emissions estimates and associated uncertainty ranges from upscaling fall within state-of-the-art model ensemble estimates from the Global Carbon Project (GCP) methane budget. In some tropical regions, the spatial pattern of UpCH4 emissions diverged from GCP predictions, however, inclusion of flux measurements from additional ground-based sites, together with refined maps of tropical wetlands extent, could reduce these prediction uncertainties

# ja-Kana

京都大学0048新制・課程博士博士(理学)甲第21332号理博第4428号新制||理||1636(附属図書館)京都大学大学院理学研究科化学専攻(主査)教授 杉山 弘, 教授 秋山 芳展, 准教授 竹田 一旗学位規則第4条第1項該当Doctor of ScienceKyoto UniversityDGA

UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258

Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5′-AABrUBrU-3′ sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA

Antiproliferative and apoptotic activities of sequence-specific histone acetyltransferase inhibitors

In parallel to monomeric epigenetic regulators, sequence-specific epigenetic regulators represent versatile synthetic dual-target ligands that achieve regulatory control over multi-gene networks. Development of DNA-binding domain (DBD)-HDAC inhibitors and DBD-HAT activators, which result in increased histone acetylation, has become one promising research field. However, there is no report regarding the gene regulatory pattern by sequence-specific epigenetic repressor. We report here for the first time, the synthesis of DBD-HAT inhibitors and demonstrate that these conjugates could retain their dual-target activity using predicted working model of thermal stability assay and in vitro HAT activity assay. Evaluation of antiproliferative activity in cancer cells showed that 2 (with a medium linker length of 13-atom) exhibited the highest antiproliferative activity in p53 wild-type cancer cell lines (IC[50] of 1.8–2.6 μM in A549 and MV4-11 cells) and not in p53 mutant cancer cell lines. A mechanistic investigation using microarray analysis and an apoptotic assay showed that the antiproliferative effect of 2 occurred via the up-regulation of p53 target genes, and the subsequent initiation of p53-dependent apoptosis. Our research on sequence-specific dual-target epigenetic repressor offers us an alternative way to modulate HAT-governed therapeutically important genes and contributes to offer a fresh insight into antitumor therapeutics

Study of heat pipe in motor cooling: A review

The heat pipe as one of the most efficient heat exchanger device is used in many thermal engineering applications. Through sufficient literature research and summary, a comprehensive and systematic analysis of the application of heat pipe cooling technology in motor cooling is provided. The basic principles and key technologies of heat pipe cooling technology is introduced. What’s more, various factors affecting the cooling efficiency of heat pipes and two main types of heat pipe applications in motor cooling are discussed. Finally, the current status of research on heat pipe cooling motors at home and abroad are reviewed

Change Detection Algorithm for Multi-Temporal Remote Sensing Images Based on Adaptive Parameter Estimation

This paper proposes a multioral image change detection algorithm based on adaptive parameter estimation, which is used to solve the problems of severe interference of coherent speckle noise and the retention of detailed information about changing regions in synthetic aperture radar remote sensing images. The change area in the initial differential image has local consistency and global prominence. By detecting the significant area to locate similar change areas, the coherent speckle noise outside the area can be eliminated. The use of hierarchical FCM clustering to automatically generate training samples can improve the reliability of training samples. In addition, in order to increase the distinction between the changed area and the non-changed area, a sparse automatic encoder is used to extract the changed features and generate a change detection map. Experiments using 4 sets of SAR images show that the algorithm can effectively reduce the effect of speckle noise on detection accuracy, the extraction of changing areas is more complete and meticulous, and the false detection rate is greatly reduced. Since the images in different time phases will be disturbed by weather, clouds, sea water, etc., the target segmentation algorithm can be used to extract the target of interest and highlight the changing area. Principal component analysis and k-means clustering method are used to reduce the influence of isolated pixels, and change information is extracted to obtain different images. The experiment uses four sets of image data of islands and reefs. The experiment proves that the algorithm can well eliminate external interference, improve the accuracy of change detection, and have a good detection effect on the area of islands and reefs. The adaptive parameter estimation plays a good role in the detection of changing areas, and the visual effect is better, which can improve the accuracy of the detection results.Optical and Laser Remote Sensin

Recent Progress of Targeted G-Quadruplex-Preferred Ligands Toward Cancer Therapy

A G-quadruplex (G4) is a well-known nucleic acid secondary structure comprising guanine-rich sequences, and has profound implications for various pharmacological and biological events, including cancers. Therefore, ligands interacting with G4s have attracted great attention as potential anticancer therapies or in molecular probe applications. To date, a large variety of DNA/RNA G4 ligands have been developed by a number of laboratories. As protein-targeting drugs face similar situations, G-quadruplex-interacting drugs displayed low selectivity to the targeted G-quadruplex structure. This low selectivity could cause unexpected effects that are usually reasons to halt the drug development process. In this review, we address the recent research on synthetic G4 DNA-interacting ligands that allow targeting of selected G4s as an approach toward the discovery of highly effective anticancer drugs

Pip-HoGu: An Artificial Assembly with Cooperative DNA Recognition Capable of Mimicking Transcription Factor Pairs

Cooperation between pairs of transcription factors (TFs) has been widely demonstrated to play a pivotal role in the spatiotemporal regulation of gene expression, but blocking cooperative TF pair–DNA interactions synergistically has been challenging. To achieve this, we designed programmable DNA binder pyrrole-imidazole polyamides conjugated to host–guest assemblies (Pip-HoGu) to mimic the cooperation between natural TF pairs. By incorporating cyclodextrin (Cyd)–adamantane (Ada), we synthesized Ada1 (PIP1-Ada) and Cyd1 (PIP2-Cyd), which were evaluated using Tm, EMSA, competitive, and SPR assays and molecular dynamics studies. The results consistently demonstrated that Pip-HoGu system formed stable noncovalent cooperative complexes, thereby meeting key criteria for mimicking a TF pair. The system also had a longer recognition sequence (two-PIP binding length plus gap distance), favorable sequence selectivity, higher binding affinity, and in particular, a flexible gap distance (0–5 bp). For example, Ada1–Cyd1 showed thermal stability of 7.2 °C and a minimum free energy of interaction of −2.32 kcal·mol⁻1 with a targeting length of 14 bp. Furthermore, cell-based evaluation validated the capability of Pip-HoGu to exhibit potent cooperative inhibitory effects on gene expression under physiological conditions by disrupting TF pair–DNA function. In conclusion, the modular design of Pip-HoGu defines a general framework for mimicking naturally occurring cooperative TF pair–DNA interactions that offers a promising strategy for applications in the precise manipulation of cell fate