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| 1 | De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation显示文摘Structural variants(SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome(ZF1), with a contig N50 length of 24.57 mega-base pairs(Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps(0.25 Mb in total length) in the reference human genome(GRCh38). Markedly, we detected17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid(Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1(1.32%–1.53%) compared to other East Asian genomes(0.70%–0.98%),reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence-a662-bp intronic insertion in the SCUBE2 gene-is enriched and associated with better lung function(the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies. | Ouzhuluobu Yaoxi He Haiyi Lou Chaoying Cui Lian Deng Yang Gao Wangshan Zheng Yongbo Guo Xiaoji Wang Zhilin Ning Jun Li Bin Li Caijuan Bai Baimakangzhuo Gonggalanzi Dejiquzong Bianba Duojizhuoma Shiming Liu Tianyi Wu Shuhua Xu Xuebin Qi Bing Su | 2020 | National Science Review2020，7，2： | 4 |
| 2 | 围术期血液稀释对高原高血红蛋白血症生命体征的影响显示文摘目的研究高海拔地区高原高血红蛋白血症围术期血液稀释对生命体征的影响。方法方便选择2012年5月-2016年5月世居迪庆州香格里拉高海拔地区居民,拟行腹腔镜胆囊切除术患者105例,分为血红蛋白正常组(N组=35例),高血红蛋白80例,高血红蛋白者分为高血红蛋白血液稀释组(SH组=35例)、高血红蛋白血液未稀释组(NH组=35例),SH组于术前3 d采用放5%循环血量(8 mL/kg),同时补充复方氯化钠液20 mL/(kg·24 h)(晶体胶体=2∶1)。结果血液稀释前,SH组和NH组患者血红蛋白(Hb)、红细胞血球压积(HCT)、全血高切粘度(WBHSV)、全血低切粘度(WBLSV)明显高于N组(P<0.05);血液稀释后,SH组患者血红蛋白(Hb)、红细胞血球压积(HCT)、全血高切粘度(WBHSV)、全血低切粘度(WBLSV)明显高于N组,但明显低于NH组(P<0.05);术中和苏醒期,与N组比较,NH和SH组患者血压、心率明显升高,与NH组比较,SH组患者血压、心率则明显降低(P<0.05);与N组(20.00%)相比,NH组患者苏醒期脱氧后SPO2<86%的发生率(85.71%)明显增高;与NH组比较,SH组患者苏醒期脱氧后SPO2<86%的发生率(48.57%)则明显下降(χ2=30.425, P<0.01)。3组患者术中吸纯氧(SPO2>95%)和心律失常事件发生率分别为100.00%、88.57%、100.00%,2.86%、11.43%、5.71%,组间差异无统计学意义(P>0.05);NH组患者术后伤口恢复时间较长(F=20.000,P<0.01)。结论术前血液稀释能降低高原高血红蛋白血症,并可明显减少患者术中和术后的血流动力学波动,并能明显改善患者术后苏醒期的氧合及恢复。 | 张茂荷 牟朝霞 陈体仙 | 2019 | 中外医疗2019，38，31： | 3 |
| 3 | Convergent adaptation of the genomes of woody plants at the land-sea interface显示文摘Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies.While such studies should shed light on molecular convergence,genomic-level analyses have been unsuccessful,due mainly to the absence of empirical controls.Woody plant species that colonized the global tropical coasts,collectively referred to as mangroves,are ideal for convergence studies.Here,we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades.To detect convergence in a large phylogeny,a CCS+model is implemented,extending the more limited CCS method(convergence at conservative sites).Using the empirical control for reference,the CCS+model reduces the noises drastically,thus permitting the identification of 73 convergent genes with Ptrue(probability of true convergence)>0.9.Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance.Importantly,convergence is more often manifested at a higher level than at amino-acid(AA)sites.Relative to>50 plant species,mangroves strongly prefer 4 AAs and avoid 5 others across the genome.AA substitutions between mangrove species strongly reflect these tendencies.In conclusion,the selection of taxa,the number of species and,in particular,the empirical control are all crucial for detecting genome-wide convergence.We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence. | Ziwen He Shaohua Xu Zhang Zhang Wuxia Guo Haomin Lyu Cairong Zhong David EBoufford Norman CDuke The International Mangrove Consortium Suhua Shi | 2020 | National Science Review2020，7，6： | 3 |
| 4 | 群体基因组学方法:从经典统计学到有监督学习显示文摘群体遗传学的一个主要研究目标是理解突变、自然选择、遗传漂变、群体结构和数量变化等进化力量如何共同影响基因组中的遗传变异.通过分析DNA序列多态数据,可以推测曾经作用于基因组的各种力量,进而探讨生物演化的过程.近年来,随着第二代DNA测序技术的快速革新,群体遗传学进入了基因组学时代,相关的方法在不断发展,并可将群体基因组学方法分为经典统计学方法和新兴的机器学习方法.前者包括经典群体遗传学统计量、单一统计量或多统计量联合检测自然选择、群体历史与自然选择的联合估计以及基于溯祖树和祖先重组图的方法.后者主要基于有监督学习,为群体基因组时代的大数据分析带来了全新范式.本文从理论基础出发,全面回顾了群体基因组学方法发展变化的历程,着重介绍了该领域的最新进展,并就未来的发展方向进行了展望. | 施怿 李海鹏 | 2019 | 中国科学:生命科学2019，49，4： | 2 |
| 5 | iNOS在大通牦牛和平原黄牛肺脏组织中增龄性表达变化研究显示文摘为了阐明大通牦牛肺脏组织中诱导型一氧化氮化酶(iNOS)随着年龄增长的变化趋势和特点,试验从青海省大通县(海拔3200 m)选取健康的1日龄、30日龄、180日龄和成年的大通牦牛作为研究对象,同时选择湖北省襄阳市(海拔约100 m)相同发育阶段的平原黄牛作为对照,采用实时荧光定量PCR和Western-blot分析,从基因和蛋白质水平对大通牦牛iNOS在不同发育阶段中的表达情况进行研究。结果表明:随着年龄增长,大通牦牛肺脏组织iNOS基因表现为先降低再升高的趋势,与成年时比较,1日龄时相对表达量最高(P<0.05),30日龄时相对表达量最低(P<0.05);平原黄牛表现为随着年龄增长逐渐降低的趋势,与成年时比较各日龄时均差异显著(P<0.05)。相同发育阶段,1日龄时大通牦牛肺脏组织iNOS基因相对表达量显著高于平原黄牛(P<0.05),30日龄时显著低于平原黄牛(P<0.05),180日龄时差异不显著(P>0.05),成年时显著高于平原黄牛(P<0.05)。肺脏组织iNOS蛋白表达,无论是不同发育阶段的变化趋势,还是相同发育阶段的表达特点,均表现出与iNOS基因表达一致的特点。说明大通牦牛肺脏中iNOS基因/蛋白的表达可能与高原低氧适应性相关。 | 秦鸿楠 周娟 万瑞东 张勤文 | 2022 | 黑龙江畜牧兽医2022，，7： | 1 |
| 6 | Heightened protein-translation activities in mammalian cells and the disease/treatment implications显示文摘After cells divide,the new cells have to synthesize all the necessary cellular components in time for the next division.There is a lower bound of time required for cells to double their contents.For mammalian cells,this lower bound may be around 20 hours,as artificial selection for faster-dividing cells has not pushed cell lines to go below this'barrier*in doubling time.The occasional exceptions are those that appear to‘prove the rule’.For example,yeast cells can divide once every 1.5 hours[1,2];and the fastest rate of cell divisions in metazoans may be that of the embryonic cells of Drosophila,at 5 minutes per cycle[3].Thus,at least for eukaryotic cells,the rate-limiting step is not the replication of DNA. | Chung-I Wu Haijun Wen | 2020 | National Science Review2020，7，12： | 0 |
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