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Single-cell and spatial omics:exploring hypothalamic heterogeneity

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Neural Regeneration Research 2025年第6期20卷 1525-1540页

作者： Muhammad Junaid Eun Jeong Lee Su Bin Lim Department of Biochemistry&Molecular Biology Ajou University School of MedicineSuwonSouth Korea Department of Biomedical sciences Graduate School of Ajou UniversitySuwonSouth Korea Department of Brain Science Ajou University School of MedicineSuwonSouth Korea

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

关键词： cellular diversity hypothalamus multi-omics single-cell transcriptomics spatial transcriptomics

Insights from an academic endeavor into central nervous system drug discovery

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Neural Regeneration Research 2025年第6期20卷 1717-1718页

作者： Lieve van Veggel An M.Voets Tim Vanmierlo Rudy Schreiber BIOMED Biomedical Research Institute Faculty of Medicine and Life SciencesHasselt UniversityHasseltBelgium Department of Psychiatry and Neuropsychology Division of Translational NeuroscienceEuropean Graduate School of NeuroscienceSchool for Mental Health and NeuroscienceMaastricht UniversityMaastrichtThe Netherlands Section of Psychopharmacology Neuropsychology and PsychopharmacologyFaculty of Psychology and NeuroscienceMaastricht UniversityMaastrichtThe Netherlands University MS Center(UMSC) Hasselt-PeltBelgium

Historically,"big pharma"did most central nervous system drug discovery R&D ***,in modern times their"management reductionism"resulted in disappointing pipelines and pharma resided to(late)development,regulatory approval,and marketing(Thong,2015).This had significant consequences for financing and executing research,resulting in a larger role for funding by governments and patient-organizations and a shift of research to academia(Mazzucato,2013).

关键词： academic approval consequences

High mobility group box 1 in the central nervous system:regeneration hidden beneath inflammation

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Neural Regeneration Research 2025年第1期20卷 107-115页

作者： Hanki Kim Bum Jun Kim Seungyon Koh Hyo Jin Cho Xuelian Jin Byung Gon Kim Jun Young Choi Department of Brain Science Ajou University School of MedicineSuwonSouth Korea Department of Biomedical sciences Ajou University Graduate School of MedicineSuwonSouth Korea Department of Neurology Ajou University School of MedicineSuwonSouth Korea Department of Geriatrics The Affiliated Suqian First People’s Hospital of Nanjing Medical UniversitySuqianJiangsu ProvinceChina

High-mobility group box 1 was first discovered in the calf thymus as a DNA-binding nuclear protein and has been widely studied in diverse fields,including neurology and ***-mobility group box 1 in the extracellular space functions as a pro-inflammatory damage-associated molecular pattern,which has been proven to play an important role in a wide variety of central nervous system disorders such as ischemic stroke,Alzheimer’s disease,frontotemporal dementia,Parkinson’s disease,multiple sclerosis,epilepsy,and traumatic brain *** drugs that inhibit high-mobility group box 1 as a damage-associated molecular pattern,such as glycyrrhizin,ethyl pyruvate,and neutralizing anti-high-mobility group box 1 antibodies,are commonly used to target high-mobility group box 1 activity in central nervous system *** it is commonly known for its detrimental inflammatory effect,high-mobility group box 1 has also been shown to have beneficial pro-regenerative roles in central nervous system *** this narrative review,we provide a brief summary of the history of high-mobility group box 1 research and its characterization as a damage-associated molecular pattern,its downstream receptors,and intracellular signaling pathways,how high-mobility group box 1 exerts the repair-favoring roles in general and in the central nervous system,and clues on how to differentiate the pro-regenerative from the pro-inflammatory *** targeting high-mobility group box 1 in the central nervous system may benefit from differentiating between the two functions rather than overall suppression of high-mobility group box 1.

关键词： central nervous system damage-associated molecular pattern ethyl pyruvate glycyrhizzin high mobility group box 1 inflammation neural stem cells neurodevelopment oligodendrocyte progenitor cells redox status regeneration

AtPEPTIDE RECEPTOR_2 mediates the AtPEPTIDE1‐induced cytosolic Ca^(2+) trise, which is required for the suppression of Glutamine Dumper gene expression in Arabidopsis roots

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Journal of Integrative Plant Biology 2014年第7期56卷 684-694页

作者： Chunli Ma Jie Guo Yan Kang Kohei Doman Anthony C.Bryan Frans E.Tax Yube Yamaguchi Zhi Qi College of life sciences Inner Mongolia University Crop Physiology Laboratory Graduate School of Agriculture Hokkaido University Department of Molecular and Cellular Biology and school of Plant sciences University of Arizona graduate school of life and Environmental sciences Osaka Prefecture University

AtPEPTIDE RECEPTOR2 （AtPEPR2） is a member of leucine-rich repeat receptor-like kinase family and binds to a group of AtPROPEP gene-encoded endogenous peptides, AtPeps. Previously, we found that AtPEPR2 plays a moderate role in the AtPep1-mediated innate immunity responses in Arabidopsis leaf. In this study, we found that AtPEPR2 promoter has strong activity in the vascular tissues of the roots and the atpepr2 mutants showed a moderate but significantly shorter root phenotype. AtPEPR2 partial y mediated AtPep1-induced root elongation inhibition. AtPep1-triggered cytosolic Ca2t transient rise in roots showed partial dependence on AtPEPR2 and ful y on extracellular Ca2t （[Ca2t]ext）. Transcriptional profiling analysis found that expression of 75% of AtPep1-modulated genes in roots was ful y dependent on AtPEPR2, of which two dramatical y induced genes showed partial dependence on the [Ca2t]ext. Arabidopsis genome contains seven Glutamine Dumpers genes （AtGDUs）, encoding amino acid exporters. Three of them （AtGDU2, 3, 5） were among the top 10 genes that were＆amp;nbsp;downregulated by AtPep1 through AtPEPR2 ful y dependent pathway. Treatment with AtPep1 strongly suppressed pro-moter activity of AtGDU3 in roots, which was relieved by chelating [Ca2t]ext. Arabidopsis overexpressing AtGDU3 showed a shorter root phenotype and decreased sensitivity to the AtPep1-mediated inhibition of root elongation. Taken together, this study demonstrated a significant role of AtPEPR2 in the AtPep1-mediated signaling in the roots.

关键词： Arabidopsis AtPeptide cytosolic Ca2+ receptor-like kinase root

Characteristics of Nutrient Salt Uptake Associated with Water Use of Corn as a Catch Crop at Different Plant Densities in a Greenhouse

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Pedosphere 2014年第3期24卷 339-348页

作者： D.YASUTAKE C.KIYOKAWA K.KONDO R.NOMIYAMA M.KITANO M.MORI S.YAMANE M.MAEDA H.NAGARE T.FUJIWARA agriculture Unit Research and Education Faculty Kochi University The United graduate school of Agricultural sciences Ehime University Faculty of agriculture Kyushu University graduate school of Environmental and life Science Okayama University

Dent corn, as a catch crop used for salt removal, was cultivated at different densities, i.e., 7.3 （low density）, 59.7 （normal density）, and 119.5 plants m-2 （high density）, during a 50 d fallow period after cultivation of a commercial crop in a greenhouse, to analyze the characteristics of nutrient salt （N, K, Mg, and Ca） uptake by roots and to study the effect of plant density on the characteristics associated with crop water use. Leaf area index for the high and normal density treatments reached extremely high values of 24.3 and 14.9, respectively. These values induced higher transpiration rates that were estimated using the Penman-Monteith model with the incorporation of specific parameters for crop and greenhouse conditions. The total N, K, Mg, and Ca contents in the crop canopy at harvest were 26.8, 13.0, 1.0, and 1.7 g m-S, respectively, under the high density treatment. The dynamics of salt uptake rates for high, normal, and low density treatments were evaluated by assessing weekly changes in salt content, and were subsequently compared against the transpiration rate. A positive linear relationship was obtained between these 2 parameters for all 3 density treatments and all tested salts. Hence, higher transpiration rates caused higher salt uptake rates through water absorption. On the other hand, salt uptake efficiency per unit water use by cultivation was lower in the low density treatment. Therefore, management procedures with dense planting that induce higher transpiration rates and lower evaporation rate are extremely important for the effective cultivation of corn catch crops.

关键词： evapotranspiration root uptake salt removal transpiration

Base flow separation for soil erosion simulation in a granitic forested headwater catchment using a process-based model, GeoWEPP

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International Journal of Sediment Research 2023年第4期38卷 494-502页

作者： Takuhei Yamasaki Shoichiro Hamamoto Taku Nishimura The graduate school of Agricultural and life sciences The University of Tokyo

Distributed erosion models, which simulate the physical processes of water flow and soil erosion, are effective for predicting soil erosion in forested catchments. Although subsurface flow through multiple pathways is dominant for runoff generation in forested headwater catchments, the process-based erosion model, Geo-spatial interface for Water Erosion Prediction Project(Geo WEPP), does not have an adequate subsurface component for the simulation of hillslope water flow. In the current study, the quick flow related to soil erosion during rainfall events is separated from the total hydrograph using base flow separation for Geo WEPP to use direct runoff to predict sediment discharge from a granitic-forested catchment in Japan. Water runoff and sediment discharge also are simulated using the conventional method that reproduces the total hydrograph, and the accuracy of the calculation and estimated erodibility parameters are evaluated. The proposed procedure reproduced the quick-flow runoff during rainfall and the cumulative sediment discharge from the catchment. Simultaneously, the proposed procedure overestimates water runoff during extreme weather events, such as typhoons. The estimated erodibility parameters for the hillslope soil were comparable to those of the surface soil in Japan using both the proposed procedure and the conventional one. Conversely, the channel erodibility obtained from the proposed procedure matched the observed sediment characteristics in the granitic forested catchment. The proposed procedure is a promising method to predict sediment discharge from forested catchments based on the geological features of the catchment.

关键词： Soil erosion Base flow separation GeoWEPP Headwater catchment Forest

Analysis of forest structural complexity using airborne LiDAR data and aerial photography in a mixed conifer–broadleaf forest in northern Japan

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Journal of Forestry Research 2018年第2期29卷 473-487页

作者： Sadeepa Jayathunga Toshiaki Owari Satoshi Tsuyuki Department of Global Agricultural sciences Graduate School of Agricultural and Life SciencesThe University of Tokyo The University of Tokyo Hokkaido Forest Graduate School of Agricultural and Life SciencesThe University of Tokyo

Determining forest structural complexity,i.e.,a measure of the number of different attributes of a forest and the relative abundance of each attribute,is important for forest management and *** this study,we examined the structural complexity of mixed conifer–broadleaf forests by integrating multiple forest structural attributes derived from airborne Li DAR data and aerial *** sampled 76 plots from an unmanaged mixed conifer–broadleaf forest reserve in northern ***-level metrics were computed for all plots using both field and remote sensing data to assess their ability to capture the vertical and horizontal variations of forest structure.A multivariate set of forest structural attributes that included three Li DAR metrics(95 th percentile canopy height,canopy density and surface area ratio) and one image metric(proportion of broadleaf cover),was used to classify forest structure into structural complexity *** results revealed significant correlation between field and remote sensing metrics,indicating that these two sets of measurements captured similar patterns of structure in mixed conifer–broadleaf ***,cluster analysis identified six forest structural complexity classes includingtwo low-complexity classes and four high-complexity classes that were distributed in different elevation *** this study,we could reliably analyze the structural complexity of mixed conifer–broadleaf forests using a simple and easy to calculate set of forest structural attributes derived from airborne Li DAR data and high-resolution aerial *** study provides a good example of the use of airborne Li DAR data sets for wider purposes in forest ecology as well as in forest management.

关键词： Airborne laser scanning High resolution imagery Hokkaido Forest structure Pan-mixed forests

Biochar and Compost Increase Crop Yields but the Effect is Short Term on Sandplain Soils of Western Australia

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Pedosphere 2015年第5期25卷 720-728页

作者： David J.M.HALL Richard W.BELL Department of agriculture and Food school of Veterinary and life sciences Murdoch University

Sandplain soils on the south coast of Western Australia have low inherent fertility, which is mainly due to poor nutrient retention caused by insufficient clay and organic colloidal material. Previous research has shown the benefits in nutrient levels and retention from adding clay to sandplain soils; however, there is almost no information on the addition of organic amendments. A field experiment was established at the Esperance Downs Research Station, Western Australian, in May 2010, to assess the effects of wheat straw(WS) and chicken manure(CM) biochars and compost with and without phosphorus(P) addition on soil properties and crop production over five growing seasons. The five seasons alternated between winter and summer crops. The CM and WS biochar and compost treatments significantly increased crop yields and P uptake in 3, 2 and 1 of the five seasons, respectively. The yield increases(P < 0.05) were no more than 8%. By the end of the third season, no differences in crop yields were found that could be attributed to the organic amendments. The addition of P increased crop yields in each winter cropping season. Phosphorus addition explained more than 30%of the variation in crop yields. Despite marginal P levels and summer drought conditions, arbuscular mycorrhizal root colonisation was not affected by the organic amendments. There were no significant interactions between the organic amendments and P addition in terms of crop yields, P uptake or P uptake efficiency. We conclude that much of the effect of the organic amendments was due to direct nutrient addition which dissipated over time.

关键词： mycorrhizal root colonisation nutrient retention organic amendments P addition P uptake

High-solids anaerobic mono-digestion of riverbank grass under thermophilic conditions

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Journal of Environmental sciences 2017年第2期29卷 29-38页

作者： Fetra J.Andriamanohiarisoamanana Nobuyuki Matsunami Takaki Yamashiro Masahiro Iwasaki Ikko Ihara Kazutaka Umetsu graduate school of Animal and Food Hygiene Obihiro University of Agriculture and Veterinary Medicine graduate school of agriculture Science Kobe University

The purpose of this study was to investigate the potential of high-solids anaerobic mono-digestion of riverbank grass under thermophilic conditions, focusing on the effects of the strength and the amount of inoculum. Ensiled grass was inoculated with three different inocula; inoculum from liquid anaerobic digester（LI）, inoculum from dry anaerobic digester（DI）, and mixture of LI and DI（MI）, at feedstock-to-inoculum ratio（FIR） of 1, 2 and 4. The ensiling process of riverbank grass reduced moisture content（p 〉 0.05）, while the hemicellulose content was significantly increased from 30.88% to 35.15%（p 〈 0.05）, on dry matter basis. The highest methane production was at an FIR of 2 with MI（167 L/kg VSadded）,which was significantly higher（p 〈 0.05） than with DI, but not significant compared to LI（p 〉 0.05）. At an FIR of 4, digesters inoculated with LI and DI failed to produce methane,whereas 135 LCH4/kg VSaddedwas obtained with MI. The kinetic studies showed that at an FIR of 1 with LI and MI, the inoculum had less of effects on the hydrolysis rate constant（0.269 day-1and 0.245 day-1） and methane production（135 versus 149 L/kg VSadded）; rather,it affected the lag phase. In a thermophilic HS-AD of riverbank grass, the mixture of inoculum with low and high total solids content（TS） helps increase the TS of inoculum and digestion process. An FIR of 2 was deducted to be the limit for a better startup time and higher volumetric productivity of methane.

关键词： Riverbank grass High-solids anaerobic digestion Inoculum Feedstock-to-inoculum ratio Thermophilic temperature