当前共找到 49 篇文献分享,本页显示第 1 - 20 篇。
1.
ZĒNG Yíngzhū (Zoo) 曾莹珠
(2025-06-30 23:51):
#paper
DOI: 10.1093/schbul/sbaf072
Schizophrenia Bulletin
2025
Candidate Targets for Resilience Training to Reduce Transdiagnostic Risk for Mental Illness.
韧性训练(RT)作为基于正念的4次团体干预,显著降低抑郁、焦虑和压力感知。RT降低情绪反应性的机制,可能适用于PTSD的早期干预。未来可以在创伤暴露被试中测试RT,评估对PTSD症状的预防效果。
Schizophrenia Bulletin,
2025-6-17.
DOI: 10.1093/schbul/sbaf072
Abstract:
Abstract Background and Hypothesis Stress sensitivity may represent an important target for resilience-promoting, preventive interventions. Resilience Training (RT) is a 4-session, group-based behavioral intervention, focusing on mindfulness-based skills, that leads …
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Abstract Background and Hypothesis Stress sensitivity may represent an important target for resilience-promoting, preventive interventions. Resilience Training (RT) is a 4-session, group-based behavioral intervention, focusing on mindfulness-based skills, that leads to reductions in psychopathology. To investigate the mechanisms of RT, the current study tested whether acquiring the skills taught in RT leads to decreases in psychopathology via reductions in one manifestation of stress sensitivity, emotion reactivity, and associated changes in hippocampal-frontal connectivity. Study Design An open trial of RT was conducted in 103 non-help-seeking young adults with mild-to-moderate psychotic experiences (PEs) and/or symptoms of depression. Transdiagnostic symptoms, emotion reactivity, and mindfulness-related skills were measured, and, in a subset of participants (n = 41), resting-state, functional magnetic resonance imaging (fMRI) data were collected, before and after completion of RT. Study Results Replicating and extending findings of prior studies of RT, significant increases in mindfulness-related RT skills and significant decreases in transdiagnostic symptoms and emotion reactivity, as well as changes in hippocampal-frontal functional connectivity, were observed following RT (all P < .02). Mediation analyses revealed that associations between the acquisition of the RT skills and decreases in symptoms (P < .006) were fully mediated by the decrease in emotion reactivity, which was also correlated with a significant pre-to-post increase in hippocampal-dorsolateral prefrontal cortex connectivity (P = .032). Conclusions RT may lead to improvements in mental health by increasing the capacity to manage day-to-day stress. Future randomized controlled trials with extended follow-up can determine whether such improvements decrease the likelihood of developing disabling mental illnesses in transdiagnostically at-risk individuals.
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2.
钟鸣
(2025-06-30 23:50):
#paper doi:10.1021/acsomega.4c11137 A 96-Well Polyacrylamide Gel for Electrophoresis and Western Blotting
提出了一种基于96孔聚丙烯酰胺凝胶的wb技术革新,通过将传统垂直电泳改为水平运行模式(类似琼脂糖凝胶操作),并采用6 mm厚凝胶(其中2 mm用于膜转移),在保持标准96孔板兼容性的同时,实现了单次实验96样本的高通量检测。该技术验证了湿转和半干转两种膜转移方法的可行性,并通过分子量标记物、重组蛋白及细胞裂解液样本证实了其适用性。尽管分子量分辨率因迁移距离缩短而略有下降,但该方法将实验成本和时间效率提升了约8倍,显著增强了生物学研究的可扩展性和结果重现性。
3.
半面阳光
(2025-06-30 23:49):
#paper DOI: 10.1002/humu.24051. Hum Mutat 2020, AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants. 这篇文章介绍了基于ACMG指南判断PVS1(very strong pathogenicity)类变异的自动化检索工具。
Human Mutation,
2020-9.
DOI: 10.1002/humu.24051
Abstract:
No abstract available.
4.
尹志
(2025-06-30 23:17):
#paper arXiv:2411.09131;Artificial Intelligence for Quantum Computing;2024;Yuri大佬带领的一篇综述,把AI用于量子计算的几个方面都做了分析和展望,虽然不是特别细致,但如果你希望量子计算能更快做出实际问题的优越性,显然不应该错过这篇综述。
arXiv,
2024-11-14T02:11:16Z.
DOI: 10.48550/arXiv.2411.09131
Abstract:
Artificial intelligence (AI) advancements over the past few years have had anunprecedented and revolutionary impact across everyday application areas. Itssignificance also extends to technical challenges within science andengineering, including the …
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Artificial intelligence (AI) advancements over the past few years have had anunprecedented and revolutionary impact across everyday application areas. Itssignificance also extends to technical challenges within science andengineering, including the nascent field of quantum computing (QC). Thecounterintuitive nature and high-dimensional mathematics of QC make it a primecandidate for AI's data-driven learning capabilities, and in fact, many of QC'sbiggest scaling challenges may ultimately rest on developments in AI. However,bringing leading techniques from AI to QC requires drawing on disparateexpertise from arguably two of the most advanced and esoteric areas of computerscience. Here we aim to encourage this cross-pollination by reviewing howstate-of-the-art AI techniques are already advancing challenges across thehardware and software stack needed to develop useful QC - from device design toapplications. We then close by examining its future opportunities and obstaclesin this space.
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5.
小年
(2025-06-30 22:31):
#paper doi:10.1182/blood.2022016033 ,Kramer, M. H., et al. Proteomic and Phosphoproteomic Landscapes of Acute Myeloid Leukemia
研究团队对 44 例急性髓系白血病(AML)患者及 6 例健康对照样本进行蛋白质组和磷酸化蛋白质组分析,构建了包含 10,651 种蛋白质和 29,201 个磷酸化位点的数据库。发现 AML 中存在广泛的转录后调控,例如 IDH1/2 突变样本中 KDM4A/B/C 组蛋白去甲基化酶蛋白丰度显著升高,但 mRNA 水平无变化。NPMc 突变样本中,核导入蛋白 KPNA4 和 KPNB1 与突变体 NPMc 结合,可能参与异常核质运输。团队通过细胞膜蛋白筛选,鉴定出 CD180 和 MRC1/CD206 在 AML 细胞表面特异性高表达,为免疫治疗提供新靶点。磷酸化分析显示,FLT3-TKD 突变通过激活 SRC 家族激酶 FGR 和 HCK 促进增殖,PML-RARA 亚型呈现独特磷酸化特征,TP53 突变样本中 S183 位点磷酸化显著增加。该研究建立了首个整合蛋白质组与磷酸化蛋白质组的 AML 多组学数据库,揭示了转录后调控和信号通路异常的关键作用,提示 CD180、MRC1/CD206 及相关通路可作为潜在治疗靶点。
Blood,
2022-9-29.
DOI: 10.1182/blood.2022016033
Abstract:
AbstractWe have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow–derived controls. After confirming …
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AbstractWe have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow–derived controls. After confirming data quality, we orthogonally validated several previously undescribed features of AML revealed by the proteomic data. We identified examples of posttranscriptionally regulated proteins both globally (ie, in all AML samples) and also in patients with recurrent AML driver mutations. For example, samples with IDH1/2 mutations displayed elevated levels of the 2-oxoglutarate–dependent histone demethylases KDM4A/B/C, despite no changes in messenger RNA levels for these genes; we confirmed this finding in vitro. In samples with NPMc mutations, we identified several nuclear importins with posttranscriptionally increased protein abundance and showed that they interact with NPMc but not wild-type NPM1. We identified 2 cell surface proteins (CD180 and MRC1/CD206) expressed on AML blasts of many patients (but not healthy CD34+ stem/progenitor cells) that could represent novel targets for immunologic therapies and confirmed these targets via flow cytometry. Finally, we detected nearly 30 000 phosphosites in these samples; globally, AML samples were associated with the abnormal phosphorylation of specific residues in PTPN11, STAT3, AKT1, and PRKCD. FLT3-TKD samples were associated with increased phosphorylation of activating tyrosines on the cytoplasmic Src-family tyrosine kinases FGR and HCK and related signaling proteins. PML-RARA–initiated AML samples displayed a unique phosphorylation signature, and TP53-mutant samples showed abundant phosphorylation of serine-183 on TP53 itself. This publicly available database will serve as a foundation for further investigations of protein dysregulation in AML pathogenesis.
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6.
白鸟
(2025-06-30 21:13):
#paper Doi:10.1146/annurev-immunol-090122-042631.AI and immunology as a new research paradigm, Annu. Rev. Immunol. 2025.
综述文章,探索AI开发预测模型和评估个人免疫状态的潜力,以检测疾病的早期迹象、预测干预反应并指导个性化健康策略。
1.免疫系统与健康:预测疾病-->个体免疫状态与疾病易感性
免疫系统失调-->疾病(生理压力传感器);免疫系统为了解健康和生态状态提供了一个信息窗口;
个体的免疫异质性是人体免疫的基本特征;
群体变异:开发免疫系统干预(疫苗,病原体, 治疗)预测模型至关重要;
人类免疫变异是人类免疫学的核心,对于开发和优化个性化干预措施和结果至关重要。
2.AI(机器学习):分析复杂的免疫数据,发现隐藏模式,
3.免疫数据+AI:个体免疫和生理健康的动态景观和轨迹;
可解释的AI模型:基于一系列个体因素(包括免疫谱、血统、年龄、性别、社会经济因素以及其他以个人免疫状态向量表示的相关信息)预测免疫反应
解读和利用人类免疫变异以及构建强大的预测模型至关重要-->机理建模;
分析重点:通过免疫设定点、免疫健康以及将免疫系统作为衡量健康状况的窗口;
4.展望:精准监测、预测和调控的未来
Nature Immunology,
2024-11.
DOI: 10.1038/s41590-024-01974-y
Abstract:
No abstract available.
7.
刘馨云
(2025-06-30 20:34):
#paper arXiv:2406.10206;Visual Imitation Enables Contextual Humanoid Control;UC Berkeley, 2024;链接:https://videomimic.net
VIDEOMIMIC 是一个从现实视频中学习上下文感知技能的类人机器人控制方法。论文提出一种 real-to-sim-to-real 模型训练管线,首次实现在无任务标签、无奖励函数、无 MoCap 情况下,仅通过日常视频即可训练并部署一个能上下楼梯、坐下、起立、越障的通用控制策略。
核心贡献:首次提出从单目日常视频中提取4D人-场景几何信息用于机器人控制学习:同时重建人体运动与环境几何(mesh);使用人体身高先验解决尺度不确定性,生成物理仿真可用的环境与动作数据。设计了多阶段 RL 策略训练管线,实现从视频到通用策略的学习:采用 MoCap 数据预训练;引入高度图作为环境输入,实现地形感知;利用 DAgger 蒸馏去除目标角依赖,训练单一策略统一执行坐起/上下楼等多任务。所学策略仅依赖机器人自身状态与 LiDAR 高度图即可在真实机器人上运行:使用 Unitree G1 部署,实现在室内外多种楼梯、草地、椅子场景下动作;在未知环境中无需任务标签,通过“地形+方向”自然触发相应行为。相较基线方法,VIDEOMIMIC 重建精度与泛化能力大幅提升:
arXiv,
2025-05-06T17:57:12Z.
DOI: 10.48550/arXiv.2505.03729
Abstract:
How can we teach humanoids to climb staircases and sit on chairs using thesurrounding environment context? Arguably, the simplest way is to just showthem-casually capture a human motion video and …
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How can we teach humanoids to climb staircases and sit on chairs using thesurrounding environment context? Arguably, the simplest way is to just showthem-casually capture a human motion video and feed it to humanoids. Weintroduce VIDEOMIMIC, a real-to-sim-to-real pipeline that mines everydayvideos, jointly reconstructs the humans and the environment, and produceswhole-body control policies for humanoid robots that perform the correspondingskills. We demonstrate the results of our pipeline on real humanoid robots,showing robust, repeatable contextual control such as staircase ascents anddescents, sitting and standing from chairs and benches, as well as otherdynamic whole-body skills-all from a single policy, conditioned on theenvironment and global root commands. VIDEOMIMIC offers a scalable path towardsteaching humanoids to operate in diverse real-world environments.
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8.
哪有情可长
(2025-06-30 20:27):
#paper Evolutionary and functional genomics of DNA methylation in maize domestication and improvement, Nature Communication, 02 November 2020,https://doi.org/10.1038/s41467-020-19333-4. DNA 甲基化是一种普遍存在的染色质特征,存在于玉米基因组中 25% 的胞嘧啶中,但在玉米驯化过程中甲基化景观的变异和进化在很大程度上仍然未知。本文中利用现代玉米、地方品种和大刍草 (Zea mays ssp. parviglumis,玉米祖先) 种群的全基因组测序 (WGS) 和全基因组亚硫酸氢盐测序 (WGBS) 数据来估计表观突变率和选择系数。结果发现在任何情况下 DNA 甲基化直接选择的证据都很弱,但在整个种群范围内确定了数千个与近期选择相关的差异甲基化区域 (DMR)。对于两个性状相关的 DMR,vgt1-DMR 和 tb1-DMR,HiChIP 数据表明,DMR 和相应下游基因之间的交互环存在于现代玉米品系 B73 中,但在大刍草中不存在。该结果有助于更好地理解作用于 DNA 甲基化模式的进化力,并表明甲基化变异在适应性进化中的作用。
Nature Communications,
2020-11-2.
DOI: 10.1038/s41467-020-19333-4
Abstract:
AbstractDNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. …
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AbstractDNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
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9.
符毓
(2025-06-30 20:19):
#paper doi:10.1038/s41467-025-59363-4 Nature Communications, 2025, Robust interface and reduced operation pressure enabled by co-rolling dry-process for stable all-solid-state batteries. 干法工艺无需使用溶剂,是一种可持续且前景广阔的全固态电池制造方法。然而,薄而坚固的固态电解质(SSE)层的实用制造设计尚未确立。本文用了一种干法工艺方法,它能增强固态电解质层从薄膜制造到电池运行的机械稳定性。
1. 通过厚的复合正极与电解质共压方法,制成薄的固态电解质与正极的复合结构,对比单独制成的固态电解质和复合正极膜
2. 这种方法制成的固态复合材料在共轧制过程中,可形成坚固的 SSE 正电极界面,有助于电池组装过程,降低机械故障风险与传统方法相比
3. 这种坚固的界面不易形成空隙,可显著提高 ASSB 在低堆叠压力(2MPa)下的循环能力(500 次循环后容量保持率大于 80%)
4. 通过将 ASSB 与法硅负极结合制作的ASSB 袋式电池,比能量可以达到为310Wh kg-1
Nature Communications,
2025-5-6.
DOI: 10.1038/s41467-025-59363-4
Abstract:
Abstract The dry-process is a sustainable and promising fabrication method for all-solid-state batteries by eliminating solvents. However, a pragmatic fabrication design for thin and robust solid-state electrolyte (SSE) layers has …
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Abstract The dry-process is a sustainable and promising fabrication method for all-solid-state batteries by eliminating solvents. However, a pragmatic fabrication design for thin and robust solid-state electrolyte (SSE) layers has not been established. Herein, we report a dry-process approach that enhances mechanical stability of SSE layers from film fabrication to cell operation. By co-rolling thick SSE and positive electrode feeds, a uniform, thin SSE layer (50 µm) and a high loading positive electrode layer (5 mAh cm−2) with high active material ratio (80 wt%) are simultaneously achieved. This SSE-positive electrode integrated film exhibits enhanced physical properties and cyclability (> 80% retention after 500 cycles) at low stack pressure (2 MPa) compared to the freestanding counterparts, attributed to reinforced and intimate SSE-positive electrode interface constructed during co-rolling process. Additionally, an all-solid-state pouch cell with high stack-level specific energy (310 Wh kg−1) and energy density (805 Wh L−1) operating at 30 °C and 5 MPa is demonstrated.
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10.
孤舟蓑笠翁
(2025-06-30 19:17):
#paper 【doi】10.1016/j.ccell.2025.04.005;【发表年份】2025年;【期刊】Cancer Cell;【标题】Immune evolution in pre-invasive lung adenocarcinoma。【内容总结】这篇论文研究了肺腺癌前驱病变进展过程中免疫微环境的动态变化,目标是找到早期干预的治疗靶点。研究者使用空间单细胞分析(成像质谱技术)和五种小鼠模型,发现TIM-3免疫检查点在癌前阶段高表达于先天免疫细胞(如巨噬细胞、树突细胞),阻断TIM-3能显著减小小鼠模型的病变尺寸,但在侵袭期无效。具体来说,他们分析了114个人类肺腺癌前驱病变样本,通过成像质谱绘制了从非典型腺瘤性增生(AAH)到侵袭性腺癌(IAC)的免疫细胞组成与空间分布变化,发现先天免疫反应在癌前阶段占主导,而适应性免疫在侵袭期增强;小鼠实验显示TIM-3阻断在癌前阶段能减少M2型巨噬细胞、增加抗原呈递树突细胞,从而抑制肿瘤进展,但该效果具有阶段特异性。
Cancer Cell,
2025-6.
DOI: 10.1016/j.ccell.2025.04.005
Abstract:
No abstract available.
11.
徐炳祥
(2025-06-29 15:16):
#paper doi: 10.1002/advs.202505823 Advanced Science, 2025, Mitigating Cell Cycle Effects in Multi-Omics Data: Solutions and Analytical Frameworks。细胞周期图谱在不同细胞类型中,或在生命过程的不同阶段可能发生显著的变化。细胞周期不同阶段基因组不同位点拷贝数的差异和表观修饰的差异可能向组学数据中注入大量误差。本文通过mESC,MEF等已经过细胞周期分选的,有丰富多组学数据的细胞类型的对比分析,发现细胞周期图谱的差异向拷贝数变异的检测中注入大量假阳性结果、掩盖了功能性DNA甲基化位点和染色质开放性位点、现有的基于单细胞RNA-seq的消除细胞周期影响的生物信息学工具效能不佳。本研究进一步展示了细胞周期图谱这一经常被忽视的协变量在多组学分析中可能起到的重要作用,细胞周期图谱的变化可能使研究结果发生重大偏倚,值得研究者们慎重对待。
Advanced Science,
2025-5-28.
DOI: 10.1002/advs.202505823
Abstract:
AbstractCell cycle structures vary significantly across cell types, which exhibit distinct phase compositions. Asynchronous DNA replication and dynamic cellular characteristics during the cell cycle result in considerable heterogeneity in DNA …
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AbstractCell cycle structures vary significantly across cell types, which exhibit distinct phase compositions. Asynchronous DNA replication and dynamic cellular characteristics during the cell cycle result in considerable heterogeneity in DNA dosage, chromatin accessibility, methylation, and expression. Nonetheless, the consequences of cell cycle disruption in the interpretation of multi‐omics data remain unclear. Here, we systematically assessed the influence of distinct cell phase structures on the interpretation of omics features in proliferating cells, and proposed solutions for each omics dataset. For copy number variation (CNV) calling, asynchronous replication timing (RT) interference induces false CNVs in cells with high S‐phase ratio (SPR), which are significantly decreased following replication timing domain (RTD) correction. Similar noise is observed in the chromatin accessibility data. Moreover, for DNA methylation and transcriptomic analyses, cell cycle‐sorted data outperformed direct comparison in elucidating the biological features of compared cells. Additionally, we established an integrated pipeline to identify differentially expressed genes (DEGs) after cell cycle phasing. Consequently, our study demonstrated extensive cell‐cycle heterogeneity, warranting consideration in future studies involving cells with diverse cell‐cycle structures. RTD correction or phase‐specific comparison could reduce the influence of cell cycle composition on the analysis of the differences observed between stem and differentiated cells.
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12.
孤舟蓑笠翁
(2025-06-29 09:36):
#paper 【doi】10.1038/s41586-025-09182-w;【发表年份】2025年;【期刊】Nature;【标题】In vivo mapping of mutagenesis sensitivity of human enhancers。【内容总结】这篇论文想搞清楚人类增强子(控制基因开关的DNA片段)中哪些小片段对胚胎发育最关键。科学家选了7个控制大脑、心脏和四肢发育的增强子,用转基因小鼠做实验:先把这些增强子切成12碱基的小块,用CRISPR技术突变每个小块,然后观察突变后胚胎器官发育的变化(主要看颜色标记的LacZ基因表达)。他们发现69%的小块突变会影响发育(60%让增强子失效,9%反而增强活性),并用机器学习模型预测出88%的关键位点与实验结果吻合。简单说就是:像拆乐高一样把增强子拆成小零件,发现大部分零件都重要,突变会搞乱发育;还训练AI模型来预测哪些零件最关键,结果挺准。主要方法包括:转基因小鼠胚胎实验(enSERT技术)、12bp块突变策略、ChromBPNet机器学习模型分析染色质开放信号、DeepLIFT算法定位关键碱基。
13.
孤舟蓑笠翁
(2025-06-29 09:18):
#paper 【doi】10.1038/s41586-025-09154-0;【发表年份】2025年;【期刊】Nature;【标题】Major expansion in the human niche preceded out of Africa dispersal。【内容总结】这篇论文研究了为什么现代人类(智人)大约5万年前能成功走出非洲并扩散到全球,而更早的非洲外扩散(如12.5万年前)却未能留下遗传痕迹。研究者通过分析非洲479个放射性定年的考古遗址(图1显示分布),结合两种古气候模型(HadCM3和PCESM),使用物种分布模型(SDMs)和广义加性模型(GAMs)量化了人类生态位变化。结果发现,从约7万年前开始,人类逐渐适应了更广泛的生境(如森林和沙漠,图4b),这种生态灵活性在5万年前达到高峰,正好与成功扩散的时间吻合。研究认为,这种生态位扩张(可能是由于技术革新或人口压力)让人类能够应对走出非洲后遇到的各种环境挑战,而早期群体因适应性不足而失败。方法上,团队通过重采样解决考古数据的时间偏差(Extended Data Fig.1),并用主成分分析量化生态位空间变化(Extended Data Fig.3)。
Nature,
2025-6-18.
DOI: 10.1038/s41586-025-09154-0
Abstract:
Abstract All contemporary Eurasians trace most of their ancestry to a small population that dispersed out of Africa about 50,000 years ago (ka)1–9. By contrast, fossil evidence attests to earlier …
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Abstract All contemporary Eurasians trace most of their ancestry to a small population that dispersed out of Africa about 50,000 years ago (ka)1–9. By contrast, fossil evidence attests to earlier migrations out of Africa10–15. These lines of evidence can only be reconciled if early dispersals made little to no genetic contribution to the later, major wave. A key question therefore concerns what factors facilitated the successful later dispersal that led to long-term settlement beyond Africa. Here we show that a notable expansion in human niche breadth within Africa precedes this later dispersal. We assembled a pan-African database of chronometrically dated archaeological sites and used species distribution models (SDMs) to quantify changes in the bioclimatic niche over the past 120,000 years. We found that the human niche began to expand substantially from 70 ka and that this expansion was driven by humans increasing their use of diverse habitat types, from forests to arid deserts. Thus, humans dispersing out of Africa after 50 ka were equipped with a distinctive ecological flexibility among hominins as they encountered climatically challenging habitats, providing a key mechanism for their adaptive success.
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翻译
14.
孤舟蓑笠翁
(2025-06-29 09:11):
#paper 【doi】10.1038/s41586-025-09151-3;【发表年份】2025年;【期刊】Nature;【标题】Morphodynamics of human early brain organoid development。【内容总结】这项研究想了解人类大脑早期发育过程中细胞外基质(ECM)如何影响脑类器官的形状变化和区域形成。科学家们开发了新技术:1)用荧光标记不同细胞结构(细胞膜、细胞骨架等),2)用光片显微镜长期观察类器官生长,3)计算机分析细胞形状变化。他们发现:1)脑类器官发育分三个阶段(快速生长、腔室融合、成熟),2)添加外源ECM(如Matrigel)能帮助形成更规则的神经上皮结构,3)缺少ECM会导致类器官发育异常,出现更多神经嵴细胞,4)ECM通过WNT和Hippo信号通路影响类器官发育。具体来说,研究团队标记了肌动蛋白、微管等结构,用显微镜追踪数周,发现ECM能促进细胞排列整齐和腔室融合;没有ECM时,YAP1蛋白会上调,激活WNT通路基因WLS,导致类器官尾部化(更像脊髓而不是大脑)。这些发现帮助我们理解ECM在人类大脑发育中的重要作用。
Nature,
2025-6-18.
DOI: 10.1038/s41586-025-09151-3
Abstract:
Abstract Brain organoids enable the mechanistic study of human brain development and provide opportunities to explore self-organization in unconstrained developmental systems1–3. Here we establish long-term, live light-sheet microscopy on unguided …
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Abstract Brain organoids enable the mechanistic study of human brain development and provide opportunities to explore self-organization in unconstrained developmental systems1–3. Here we establish long-term, live light-sheet microscopy on unguided brain organoids generated from fluorescently labelled human induced pluripotent stem cells, which enables tracking of tissue morphology, cell behaviours and subcellular features over weeks of organoid development4. We provide a novel dual-channel, multi-mosaic and multi-protein labelling strategy combined with a computational demultiplexing approach to enable simultaneous quantification of distinct subcellular features during organoid development. We track actin, tubulin, plasma membrane, nucleus and nuclear envelope dynamics, and quantify cell morphometric and alignment changes during tissue-state transitions including neuroepithelial induction, maturation, lumenization and brain regionalization. On the basis of imaging and single-cell transcriptome modalities, we find that lumenal expansion and cell morphotype composition within the developing neuroepithelium are associated with modulation of gene expression programs involving extracellular matrix pathway regulators and mechanosensing. We show that an extrinsically provided matrix enhances lumen expansion as well as telencephalon formation, and unguided organoids grown in the absence of an extrinsic matrix have altered morphologies with increased neural crest and caudalized tissue identity. Matrix-induced regional guidance and lumen morphogenesis are linked to the WNT and Hippo (YAP1) signalling pathways, including spatially restricted induction of the WNT ligand secretion mediator (WLS) that marks the earliest emergence of non-telencephalic brain regions. Together, our work provides an inroad into studying human brain morphodynamics and supports a view that matrix-linked mechanosensing dynamics have a central role during brain regionalization.
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15.
孤舟蓑笠翁
(2025-06-29 09:01):
#paper 【doi】;【发表年份】2025年;【期刊】Nature;【标题】Targeting de novo purine biosynthesis for tuberculosis treatment。【内容总结】这篇研究想解决结核病治疗中药物耐药和疗程长的问题,科学家们发现了一种叫JNJ-6640的新药,它能精准打击结核菌制造嘌呤(DNA的原料)的第一步关键酶PurF。他们先筛了4924种化合物找到苗头,再改进结构让药效更强(MIC90=8.6 nM),用基因敲除、显微镜看细菌分裂、测肺里化学物质浓度等方法证明这药只杀结核菌不伤人类细胞。重要发现包括:药能让结核菌的DNA复制停工(看图3的细菌分裂动画),肺里的嘌呤原料太少救不了被药打击的细菌(表1数据),动物实验用长效针剂打两针就能减少近99%病菌。这药还能替换现有方案里毒性大的药物,可能让未来治疗更短更安全。简单说就是:找到新靶点→设计特效药→证明它管用且安全→能改进现有疗法。
16.
孤舟蓑笠翁
(2025-06-29 08:54):
#paper 【doi】10.1038/s41586-025-09160-2;【发表年份】2025年;【期刊】Nature;【标题】Machine-learning design of ductile FeNiCoAlTa alloys with high strength。【内容总结】这篇论文的目标是开发同时具备高强度和高延展性的新型合金,突破传统合金强度与延展性此消彼长的限制。研究者采用机器学习结合领域知识(如原子尺寸错配最大化、L12/B2相调控)设计了Fe35Ni29Co21Al12Ta3高熵合金,通过冷轧和热处理工艺获得含66.6% L12纳米沉淀相和15% B2微米相的双相结构。实验结果惊人:屈服强度达1.8GPa的同时保持25%均匀延伸率,远超现有钢材和传统高熵合金。具体而言,团队首先构建包含20种物理特征的数据库,通过六步主动学习循环(数据收集→物性描述符筛选→模型训练→知识引导虚拟筛选→效用函数设计→实验验证)优化成分,最终材料中L12相提供主要强化(859MPa),可变形B2相通过位错积累维持高加工硬化率,两者协同作用使性能突破现有材料极限。关键创新在于机器学习指导下的多组元沉淀相设计,以及通过高体积分数可变形B2相(传统硬脆相经Ta合金化后变为韧性相)实现强度-延展性协同提升。
17.
孤舟蓑笠翁
(2025-06-29 08:37):
#paper 【doi】10.1038/s41586-025-09190-w;【发表年份】2025年;【期刊】Nature;【标题】Kupffer cell programming by maternal obesity triggers fatty liver disease。【内容总结】这篇论文研究了母亲肥胖如何通过影响胎儿肝脏中的Kupffer细胞(KC)导致后代成年后出现脂肪肝疾病。简单来说,科学家发现肥胖母亲体内的高脂肪饮食会让胎儿KC细胞从正常代谢模式(氧化磷酸化)转变为异常模式(糖酵解),这种变化会持续到成年并促进肝细胞脂肪堆积。他们用小鼠实验证明,通过基因敲除KC中的HIF1α蛋白可以阻止这种代谢转变,从而预防脂肪肝。主要方法包括:建立母体肥胖小鼠模型、流式细胞术分析免疫细胞、RNA测序分析基因表达、单细胞多组学测序(RNA+ATAC)、脂质组学和代谢组学分析、体外肝细胞共培养实验等。详细来说,研究发现母体肥胖会重编程KC细胞的代谢和免疫功能,使其分泌更多载脂蛋白(如APOE和APOA1),这些蛋白会促进肝细胞吸收脂质;通过KC特异性基因敲除和细胞移植实验证实,发育期KC的异常编程是导致成年脂肪肝的关键因素,而补充正常KC可以逆转这一过程。
18.
sqc
(2025-06-28 15:11):
#paper
【doi】10.1038/s41590-024-01932-8
【发表年份】2024年
【期刊】Nature Immunology
【标题】Tumor editing suppresses innate and adaptive antitumor immunity and is reversed by inhibiting DNA methylation
【内容总结】
这篇论文研究了肿瘤在发生过程中通过基因调控逃避免疫监视的机制,并探索了DNA甲基化抑制剂恢复免疫控制的可能性。研究人员使用转基因乳腺癌小鼠模型,比较了早期(5–10天)和晚期(30–35天)肿瘤的单细胞RNA测序结果,发现晚期肿瘤中主要下调的是固有免疫和适应性免疫相关基因,特别是干扰素信号通路和相关刺激基因(ISGs),而与增殖相关的恶性基因表达几乎不变。进一步实验表明,DNA甲基化抑制剂低剂量地西他滨(decitabine, DAC)可以逆转这些免疫基因的沉默,显著抑制肿瘤生长,提高肿瘤浸润性T细胞(CD8+、CD4+、NK细胞)的数量、功能和记忆性,并降低免疫抑制性髓系细胞比例。此外,DAC能诱导肿瘤细胞中坏死性凋亡和焦亡相关基因(如Ripk3、Gsdmd、Gsdme)的表达和炎性细胞死亡,从而增强免疫清除效应。简单说就是,肿瘤通过DNA甲基化沉默免疫基因逃避免疫,而抑制甲基化可以“解锁”这些免疫通路,重新激活对肿瘤的天然和适应性免疫控制。
19.
李翛然
(2025-06-28 14:03):
#paper Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction http://jeremywohlwend.com/assets/boltz2.pdf mit最新发布的一个全原子预测模型。 我个人觉得效果并没有显著超越af3 和protenix 但是新闻吹的很多。大家可以用一用,测试一下
bioRxiv,
2025-6-18.
DOI: 10.1101/2025.06.14.659707
Abstract:
AbstractAccurately modeling biomolecular interactions is a central challenge in modern biology. While recent advances, such as AlphaFold3 and Boltz-1, have substantially improved our ability to predict biomolecular complex structures, these …
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AbstractAccurately modeling biomolecular interactions is a central challenge in modern biology. While recent advances, such as AlphaFold3 and Boltz-1, have substantially improved our ability to predict biomolecular complex structures, these models still fall short in predicting binding affinity, a critical property underlying molecular function and therapeutic efficacy. Here, we present Boltz-2, a new structural biology foundation model that exhibits strong performance for both structure and affinity prediction. Boltz-2 introduces controllability features including experimental method conditioning, distance constraints, and multi-chain template integration for structure prediction, and is, to our knowledge, the first AI model to approach the performance of free-energy perturbation (FEP) methods in estimating small molecule–protein binding affinity. Crucially, it achieves strong correlation with experimental readouts on many benchmarks, while being at least 1000×more computationally efficient than FEP. By coupling Boltz-2 with a generative model for small molecules, we demonstrate an effective workflow to find diverse, synthesizable, high-affinity binders, as estimated by absolute FEP simulations on the TYK2 target. To foster broad adoption and further innovation at the intersection of machine learning and biology, we are releasing Boltz-2 weights, inference, and training code1under a permissive open license, providing a robust and extensible foundation for both academic and industrial research.
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20.
颜林林
(2025-06-28 13:06):
#paper doi:10.1016/j.cell.2025.06.003, Cell, 2025, A host organelle integrates stolen chloroplasts for animal photosynthesis. 很多年前就听说过这个神奇的动物,海蜗牛(也叫做海牛、海兔、海蛞蝓),它吃植物,能够把吃掉的植物体内的叶绿体收为己用,以至于它自己能依靠光合作用存活。关于它的研究,上周竟然还能登上Cell顶刊,让我好奇了一番。研读下来,这确实是一篇内容详实的工作,涵盖从宏观动物个体的观察(诸如对比是否光合,两者的存活时间差别),到细胞层面(采用共聚焦显微镜、膜片钳等技术,研究其形态、电生理等特性),到分子层面(采用转录组(高通量测序)、蛋白组(质谱))。其中对这些叶绿体是如何被存储的,进行了比较深入的研究,确定并命名了“kleptosomes”("klepto-"前缀表示“偷窃”,中文或许可以翻译为“窃质体”?)这个细胞器,这应该是最大的创新点和价值,应该也是能发在顶刊上的重要原因。此外,文章还探讨了同样能够利用植物光合作用的珊瑚(与藻类形成共生关系),说明两个物种之间存在的趋同进化。文章(应该是)共享了数据和代码(见“Data and code availability”),代码需要“available from the lead contact upon request”,数据则是放在SRA上(PRJNA1187635),奇怪的是这些编号目前在SRA上还查不到,不知道是数据更新周期的问题,还是其他限制原因所致。let's wait and see.
Cell,
2025-6.
DOI: 10.1016/j.cell.2025.06.003
宿主细胞器整合被盗的叶绿体用于动物光合作用
Abstract:
No abstract available.