A field guide to the proteomics of post-translational modifications in DNA repair

All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.     

我国三大城市群地区城市和农业用地地表热环境效应对比研究

以大中小城市协同发展为特征的城市群已成为我国城市化发展的主要形式,城市化和农业作为城市群地区最主要的土地利用活动,其气候效应是国际研究的热点。然而过去研究多关注大城市的热岛效应,对更为普遍的农业活动以及中小城市城市化的气候效应认识十分薄弱。基于MODIS地表温度数据,以自然林地为参照,提出了一种可逐像元估算土地利用地表热环境效应的新方法,进而对比分析了我国三大城市群地区（京津冀、长三角和珠三角）城市和农业用地地表热环境效应及其驱动因子差异。结果表明各城市群白天城市热岛效应明显,地级以上城市年平均热岛强度达3.2℃以上,但最强热岛均未发生在核心城市。夜晚热岛效应明显减弱,京津冀和长三角部分城市甚至出现冷岛效应。农业用地在白天亦表现出明显的增温效应,特别是在京津冀地区,而在夜晚除珠三角城市群外,降温效应明显,京津冀和长三角地区平均降温2.3℃和0.7℃。虽然城市用地平均增温强度大于农业用地,但农业用地因面积优势对区域温度变化起控制作用。白天城市和农业用地整体导致各城市群温度明显增加,京津冀增温最高（4.0℃）,夜晚二者导致长三角和京津冀地区平均温度降低。研究还发现各城市群城市和农业用地地表热环境效应时空异质性极大,主要受植被、地表反照率、气候背景和人口密度控制。本文对制定缓解气候变化的土地利用策略具有重要的指导意义。     

Hyperkalaemia,not apoptosis,accurately predicts insect chilling injury

There is a growing appreciation that insect distribution and abundance are associated with the limits of thermal tolerance, but the physiology underlying thermal tolerance remains poorly understood. Many insects, like the migratory locust (Locusta migratoria), suffer a loss of ion and water balance leading to hyperkalaemia (high extracellular [K⁺]) in the cold that indirectly causes cell death. Cells can die in several ways under stress, and how they die is of critical importance to identifying and understanding the nature of thermal adaptation. Whether apoptotic or necrotic cell death pathways are responsible for low-temperature injury is unclear. Here, we use a caspase-3 specific assay to indirectly quantify apoptotic cell death in three locust tissues (muscle, nerves and midgut) following prolonged chilling and recovery from an injury-inducing cold exposure. Furthermore, we obtain matching measurements of injury, extracellular [K⁺] and muscle caspase-3 activity in individual locusts to gain further insight into the mechanistic nature of chilling injury. We found a significant increase in muscle caspase-3 activity, but no such increase was observed in either nervous or gut tissue from the same animals, suggesting that chill injury primarily relates to muscle cell death. Levels of chilling injury measured at the whole animal level, however, were strongly correlated with the degree of haemolymph hyperkalaemia, and not apoptosis. These results support the notion that cold-induced ion balance disruption triggers cell death but also that apoptosis is not the main form of cell damage driving low-temperature injury.     

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

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分子生物学技术在热泉地质微生物学研究中的应用

陆地热泉是一类典型的极端生命-环境互作的地质系统,是我们认识生命与环境协同演化的天然实验室。然而,受限于有限的研究手段,热泉中仍存在大量未解密的微生物"暗物质"。这种困境随着技术的革新得到了改善,尤其是近几年来基于组学、探针和同位素标记的多元化检测手段在嗜热微生物多样性的挖掘、新物种和新代谢途径的发现以及嗜热微生物对元素地球化学循环的调控和响应等方面取得了一系列令人瞩目的研究成果,使得热泉极端微生物和地质环境内在联系的研究也成为地质微生物学研究的热点。立足于前人研究成果,本文将简述常用于热泉地质微生物学研究的分子生物学手段的发展,重点总结其在挖掘热泉微生物多样性和热泉微生物的环境功能研究中的应用及进展,最后对未来研究方向提出展望。     

遥感技术在鸟类生态学研究中的应用

获取鸟类活动及生境信息是鸟类生态学研究的基础, 而遥感技术弥补了传统野外调查方法的缺陷, 提供了获取多种信息的新途径。应用遥感技术的鸟类生态学研究热点从最初的种群行为观察, 到栖息地选择, 再到生境适宜性、破碎化及人为干扰探究等, 随着技术的不断发展也在扩展和变化。不同波段或组合下的遥感技术各有所长。光学遥感应用广泛, 尤其是信息量较大的红外波段图像和作为野外鸟巢及物种活动监测常用工具的红外相机; 多光谱图像常用于栖息地制图以及地物识别, 高空间分辨率的数据甚至可对鸟类种群进行直接计数; 高光谱数据则可对光谱特征相似的地物进行更为精确的区分和反演; 激光雷达遥感主要用于栖息地植被结构的三维探测, 为了解鸟类栖息地选择提供更好的依据。微波遥感在飞鸟探测上应用颇多, 近年来多极化数据在复杂栖息地精确制图上也具有优势, 但成本较高、解译复杂且推广度较低。在实际应用中, 遥感数据时空尺度的选择会影响研究结果, 部分遥感反演参数也缺乏生态学意义。多源遥感数据的结合应用能够提升制图分类的精度, 实现数据的时空分辨率互补, 优化鸟类生态研究所需参数。未来的遥感技术在鸟类生态学中的应用应致力于提供更加明确的光谱信息、相对简便的解译方法, 以及更为合理的多源数据组合方式等。     

Hydrogen and oxygen trapping at the H-cluster of [FeFe]-hydrogenase revealed by site-selective spectroscopy and QM/MM calculations

[FeFe]-hydrogenases are superior hydrogen conversion catalysts. They bind a cofactor (H-cluster) comprising a four-iron and a diiron unit with three carbon monoxide (CO) and two cyanide (CN^?) ligands. Hydrogen (H₂) and oxygen (O₂) binding at the H-cluster was studied in the C169A variant of [FeFe]-hydrogenase HYDA1, in comparison to the active oxidized (Hox) and CO-inhibited (Hox-CO) species in wildtype enzyme. ⁵⁷Fe labeling of the diiron site was achieved by in vitro maturation with a synthetic cofactor analogue. Site-selective X-ray absorption, emission, and nuclear inelastic/forward scattering methods and infrared spectroscopy were combined with quantum chemical calculations to determine the molecular and electronic structure and vibrational dynamics of detected cofactor species. Hox reveals an apical vacancy at Fe_d in a [4Fe4S-2Fe]^3 ? complex with the net spin on Fe_d whereas Hox-CO shows an apical CN^? at Fe_d in a [4Fe4S-2Fe(CO)]^3 ? complex with net spin sharing among Fe_p and Fe_d (proximal or distal iron ions in [2Fe]). At ambient O₂ pressure, a novel H-cluster species (Hox-O₂) accumulated in C169A, assigned to a [4Fe4S-2Fe(O₂)]^3 ? complex with an apical superoxide (O₂^?) carrying the net spin bound at Fe_d. H₂ exposure populated the two-electron reduced Hhyd species in C169A, assigned as a [(H)4Fe4S-2Fe(H)]^3 ? complex with the net spin on the reduced cubane, an apical hydride at Fe_d, and a proton at a cysteine ligand. Hox-O₂ and Hhyd are stabilized by impaired O₂^– protonation or proton release after H₂ cleavage due to interruption of the proton path towards and out of the active site.     

Structural variability of DNA-containing Mg-pyrophosphate microparticles: optimized conditions to produce particles with desired size and morphology

Our previous studies demonstrated the formation of structurally diverse DNA-containing microparticles (DNA MPs) in PCR with Mg-pyrophosphate (MgPPi) as the structure-forming component. These DNA MPs were referred to major structural types: microdisks (2D MPs) with nanometer thickness and 3D MPs with sophisticated morphology and constructed from intersecting disks and their segments. Little is known about factors that influence both the morphology and size of DNA MPs, and the present study was aimed at fulfilling this gap. We showed that the addition of Mn²⁺ cations to PCR mixtures caused the profound changes in MPs morphology, depending on DNA polymerase used (KlenTaq or Taq). Asymmetric PCR with 20-fold decrease in the concentration of one of two primers facilitated the predominant formation of microdisks with unusual structure. The addition of 1 mM Na-pyrophosphate to PCR mixtures with synthesized DNA and subsequent thermal cycling (10–15 cycles) were optimal to produce microdisks or nanometer 3D particles. Using electron microscopy, we studied also the structure of inorganic micro- and nanoparticles from MgPPi, formed during multiple heating and cooling cycles of a mixture of Mg²⁺ and Na-pyrophosphate in various regimes. Also, we found the conditions to yield planar (Mg·Mn)PPi nanocrystals (diameter ~100 nm and thickness ~10 nm) which efficiently adsorbed exogenous DNA. These inorganic nanoparticles are promising for DNA delivery in transfection studies. Mechanisms to be involved in structural modifications of MPs and perspectives of their practical application are discussed.