Base excision repair but not DNA double‐strand break repair is impaired in aged human adipose‐derived stem cells

The decline in DNA repair capacity contributes to the age‐associated decrease in genome integrity in somatic cells of different species. However, due to the lack of clinical samples and appropriate tools for studying DNA repair, whether and how age‐associated changes in DNA repair result in a loss of genome integrity of human adult stem cells remains incompletely characterized. Here, we isolated 20 eyelid adipose‐derived stem cell (ADSC) lines from healthy individuals (young: 10 donors with ages ranging 17–25 years; old: 10 donors with ages ranging 50–59 years). Using these cell lines, we systematically compared the efficiency of base excision repair (BER) and two DNA double‐strand break (DSB) repair pathways—nonhomologous end joining (NHEJ) and homologous recombination (HR)—between the young and old groups. Surprisingly, we found that the efficiency of BER but not NHEJ or HR is impaired in aged human ADSCs, which is in contrast to previous findings that DSB repair declines with age in human fibroblasts. We also demonstrated that BER efficiency is negatively associated with tail moment, which reflects a loss of genome integrity in human ADSCs. Mechanistic studies indicated that at the protein level XRCC1, but not other BER factors, exhibited age‐associated decline. Overexpression of XRCC1 reversed the decline of BER efficiency and genome integrity, indicating that XRCC1 is a potential therapeutic target for stabilizing genomes in aged ADSCs.     

The protective effects of C16 peptide and angiopoietin-1 compound in lipopolysaccharide-induced acute respiratory distress syndrome

C16 peptide and angiopoietin-1 (Ang-1) have been found to have anti-inflammatory activity in various inflammation-related diseases. However, their combined role in acute respiratory distress syndrome (ARDS) has not been investigated yet. The objective of this study was to investigate the effects of C16 peptide and Ang-1 in combination with lipopolysaccharide (LPS)-induced inflammatory insult in vitro and in vivo. Human pulmonary microvascular endothelial cells and human pulmonary alveolar epithelial cells were used as cell culture systems, and an ARDS rodent model was used for in vivo studies. Our results demonstrated that C16 and Ang-1 in combination significantly suppressed inflammatory cell transmigration by 33% in comparison with the vehicle alone, and decreased the lung tissue wet-to-dry lung weight ratio to a maximum of 1.53, compared to 3.55 in the vehicle group in ARDS rats. Moreover, C  +  A treatment reduced the histology injury score to 60% of the vehicle control, enhanced arterial oxygen saturation (SO₂), decreased arterial carbon dioxide partial pressure (PCO₂), and increased oxygen partial pressure (PO₂) in ARDS rats, while also improving the survival rate from 47% (7/15) to 80% (12/15) and diminishing fibrosis, necrosis, and apoptosis in lung tissue. Furthermore, when C  +  A therapy was administered 4 h following LPS injection, the treatment showed significant alleviating effects on pulmonary inflammatory cell infiltration 24 h postinsult. In conclusion, our in vitro and in vivo studies show that C16 and Ang-1 exert protective effects against LPS-induced inflammatory insult. C16 and Ang-1 hold promise as a novel agent against LPS-induced ARDS. Further studies are needed to determine the potential for C16 and Ang-1 in combination in treating inflammatory lung diseases.     

TREEasy: An automated workflow to infer gene trees,species trees,and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ).     

Effect of woody plant expansion on decomposition of fine root mixtures in a grass-dominated temperate wetland

Wetlands Ecology and Management - Little is known about the effect of woody plant expansion on decomposition of root mixtures in grass-dominant temperate wetlands. Here, we collected fine roots...     

四川黑竹沟地区非飞行小型兽类物种多样性与群落组成

四川黑竹沟国家级自然保护区位于生物多样性丰富的凉山山系, 在保护和维持区域生物多样性方面具有极其重要的地位, 然而对该自然保护区兽类群落的研究却极为缺乏。为了了解该自然保护区及周边的小型兽类群落,本文作者在2018年4-10月调查了该区域的非飞行小型兽类物种多样性及其群落组成。在海拔1,537-3,830 m间共设置样方184个, 布设鼠夹9,016铗日, 捕获小型兽类536只, 隶属4目7科13属21种。包括滇攀鼠(Vernaya fulva)和等齿鼩鼹(Uropsilus aequodonenia)两个稀有物种在内的共计9个物种为该地区首次报道, 丰富了物种分布记录。结合历史资料, 黑竹沟地区共记录小型兽类43种, 隶属4目9科28属。在43种小型兽类中, 东洋界物种37种, 占绝对优势(86%), 分布型以喜马拉雅-横断山型占优, 为18种(占东洋界48.6%)。本次调查捕获的21种小型兽类中, 群落优势种为中华姬鼠(Apodemus draco, 33.2%)、北社鼠(Niviventer confucianus, 21.3%)和中华绒鼠(Eothenomys chinensis, 12.7%)。随着海拔上升, 群落优势种组成发生变化, 由北社鼠 + 中华姬鼠 + 针毛鼠(Niviventer fulvescens) + 短尾鼩(Anourosorex squamipes)群落, 转变为中华绒鼠 + 中华姬鼠 + 凉山沟牙田鼠(Proedromys liangshanensis) + 西南绒鼠(Eothenomys custos)群落。群落物种区系的分布型组成随着海拔升高而发生变化, 喜马拉雅-横断山型物种随海拔升高所占比例增大; 分布于喜马拉雅-横断山的特有种分布的下限、中点和上限平均海拔都高于非特有种, 且特有种和非特有种的中点和下限平均海拔差异显著(n = 21, df = 19, P = 0.013; n = 21, df = 19, P < 0.01), 说明该区域物种具有明显的东洋界特征, 中高海拔主要由特有种构成。本研究丰富了黑竹沟地区小型兽类及群落多样性的数据资料, 有利于该地区物种多样性的研究和保护。     

Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of Cupressus chengiana, to assess population genomics across the species' full range, comprising the Daduhe River (DDH), Minjiang River (MJR) and Bailongjiang River (BLJ) catchments in western China. admixture , principal components analysis and phylogenetic analyses indicated that each region contains a distinct lineage, with high levels of differentiation between them (DDH, MJR and BLJ lineages). MJR was newly distinguished compared to previous surveys, and evidence including coalescent simulations supported a hybrid origin of MJR during the Quaternary. Each of these three lineages should be recognized as an evolutionarily significant unit (ESU), due to isolation, differing genetic adaptations and different demographic history. Currently, each ESU faces distinct threats, and will require different conservation strategies. Our work shows that population genomic approaches using HTS can reconstruct the complex evolutionary history of threatened species in mountainous regions, and hence inform conservation efforts, and contribute to the understanding of high biodiversity in mountains.     

市县级限制开发区环境功能区划研究——以河北省张家口市为例

限制开发地区是我国主体功能区划中划定的提供重要生态功能和农产品的地区,对其进行环境功能区划对于推动环境功能区划制度落地与实施,以及限制开发区的保护与发展有着重要意义。当前国家及省级的环境功能区划研究已经相对成熟,而市县尺度的限制开发地区环境功能区划相关研究较少。在总结现有环境功能区划研究方法的基础上,以河北省张家口市为例,探讨了市县级限制开发地区环境功能区划体系设计和技术方法,提出了以公里格网作为分析单元,结合县域行政边界,基于环境功能综合评价的结果,从自然生态安全、维护人群健康和区域环境支撑能力等3个方面,开展环境功能区划。基于该方法,将张家口市分为自然生态保留区、生态功能保持区、生态功能恢复区、农产品安全保障区、环境开发准入区、聚居发展维护区6类环境功能区,并根据各环境功能区的主要功能及生态环境特点提出相应的发展建议,以期为该区域管理提供可行的操作手段。本文提出的方法也可为其他限制开发地区的环境功能区划提供参考。     

干旱胁迫对群众杨光合特性与器官干物质分配的影响

土壤干旱是北方地区杨树人工林生长和生态效益的重要限制因子。以群众杨(Populus×popularis‘35-44’)扦插苗为研究材料,采用盆栽称重法控制土壤水分,设置正常供水、中度干旱、重度干旱3种水分梯度。分别于2016年9月与2017年9月测定叶片气体交换参数、各器官干重、根冠比、叶经济性状等指标,研究了持续2年干旱胁迫下群众杨扦插苗光合特性与器官干物质分配的变化规律,分析了土壤干旱程度、树龄在"小老树"形成中的作用过程。2016年与2017年中度、重度干旱胁迫下功能叶净光合速率(P_n)受到非气孔限制,与正常供水相比分别降低了36.08%、56.42%;18.47%、5.13%。第一年干旱胁迫下群众杨气孔导度(G_s)和蒸腾速率(T_r)显著降低;第二年干旱胁迫下G_s与正常供水无显著差异,而T_r显著提高,有利于叶片C、N元素的运输分配进而维持较高的P_n。第一年随干旱胁迫程度加剧,群众杨叶片C/N显著提高,光合产物分配趋向于叶器官。第二年中度干旱胁迫下叶片C/N与正常供水相比无显著差异,各器官干重下降幅度均低于2016年,而根冠比显著增加,表明其光合产物主要用于地下部构建以适应中度干旱环境;持续重度干旱则光合产物向茎中的分配比例提高。干旱胁迫导致群众杨功能叶水分利用效率(WUE,Water use efficiency)与光合氮利用效率(PNUE,Photosynthetic nitrogen use efficiency)显著降低,整株氮利用效率(NUE,Whole plant nitrogen use efficiency)显著提高。严重土壤干旱下叶片耗水增强、PNUE下降以及茎木质部碳投资增加可能是群众杨小老树形成的重要原因。     

京津冀城市群土地利用变化对地表径流的影响

城市化的显著特征之一是地表景观格局被人为改变,大量硬化地表覆盖、取代了原本自然或半自然的土地覆盖类型,极大地干扰了区域水文循环过程。其中,最直接的体现是对地表径流过程的影响。城市群作为当前我国城市化的重要模式,其聚集连片的扩张模式,对区域地表径流过程的干扰尤为严重。以京津冀特大城市群为研究区域,应用长期水文影响评价模型(L-THIA),以1980、1990、2000、2010、2015年5期土地利用数据、土壤数据以及1950—2015年逐日降雨数据为输入,模拟计算了不同土地利用/覆被格局对多年平均地表径流量的影响。结果表明,(1)经过率定的L-THIA模型能够较为准确地模拟京津冀城市群地区的地表径流分布特征,模型模拟误差在±10%内;(2)1980—2015年,京津冀城市群地区不透水地表面积急剧增加,其净增长值为12690.14 km~2。北京与天津等超大城市不透水地表面积增加最明显;(3)随着土地利用格局的变化,京津冀地区地表径流量呈逐年增长趋势。1980—2015年,京津冀城市群地区地表径流量的绝对增长值为17.84亿m~3,增幅11.83%。其中,1990—2000年及2010—2015年期间地表径流年均增长率较大,分别为0.36%与0.46%。对地表径流贡献较大的土地利用类型为耕地和不透水地表,其5期土地利用情景下的平均产流占比分别为35.38%、22.71%;(4)城市尺度上,不同城市的标准化年均径流深(NAARD)存在较大差异。天津、石家庄的产流能力较强,承德、衡水等城市的产流能力较弱,北京市的标准化年均径流深处于中等水平。另一方面,不同城市标准化年均径流深增长规律也存在较大差异。1980—2015年,天津市的NAARD增长最多,承德市增长最少,北京市的NAARD增长处于中等水平。本文对于京津冀城市群水文过程的时空演变研究以及国土空间优化指导具有参考意义。     

The correlation of microRNA-499 rs3746444 T>C locus with the susceptibility of gastric cancer: from a case–control study to a meta-analysis

The relationship between rs3746444 T>C single-nucleotide polymorphism (SNP) in microRNA (mir)-499 and risk of gastric cancer (GC) has been widely investigated. However, the association was still unconfirmed. Here, we first recruited 490 GC patients and 1476 controls, and conducted a case-control study. And we did not find any association between rs3746444 T>C SNP polymorphism and risk of GC. Subsequently, we conducted a meta-analysis to explore the association of mir-499 rs3746444 polymorphism with GC development. Two authors searched the PubMed and EMBASE databases up to October 15, 2019 independently. Finally, nine literatures involving 12 independent studies were included. In total, 3954 GC cases and 9745 controls were recruited for meta-analysis. The results suggested that allele model, homozygote model and recessive model could increase the risk of overall GC (P = 0.002, 0.009 and 0.013, respectively). When we excluded the studies violated HWE, this association was also found in allele model (P = 0.020) and dominant model (P= 0.044). In subgroup analyses, we identified that rs3746444 SNP in mir-499 increased the risk of GC in Asians and gastric cardiac adenocarcinoma (GCA) subgroups. No significant bias of selection was found (all P>0.1). Test of sensitivity analysis indicated that our findings were stable. Additionally, we found that the power value was 0.891 in the allele model, suggesting the reliability of our findings. In summary, our analysis confirmed the association between rs3746444 and the risk of GC, especially in Asians and in patients with GCA.