细胞重编程：再生医学研究的革命性突破——写在2012年诺贝尔生理学或医学奖颁布之际

1 2012年诺贝尔生理学或医学奖2012年10月8日,瑞典皇家科学院诺贝尔奖委员会宣布将2012年度诺贝尔生理学或医学奖(The Nobel Prize in Physiology or Medicine)授予英国发育生物学家约翰.戈登(John Bertrand Gurdon)和京都大学物质-细胞统合系统据点iPS细胞研究中心主任长山中伸弥(Shinya Yamanaka),以表彰他们"发现成熟体细胞可被重编程恢复多能性",即体细     

免疫检查点疗法：战胜癌症的革命性突破 ——写在2018年诺贝尔生理学或医学奖颁布之际

美国免疫学家詹姆斯·艾利森(James P．Allison)与日本免疫学家本庶佑(Tasuku Honjo)因在免疫检查点治疗方面的贡献而获得了2018年诺贝尔生理学或医学奖．这一发现为免疫治疗开启了一扇新的大门．本文回顾了免疫检查点CTLA-4和PD-1的研究历史,免疫检查点药物的研发和应用进展以及免疫检查点疗法在国内的发展现况,提出了免疫检查疗法目前存在的局限性和解决方法．随着近年来我国在免疫治疗领域巨大的资金投入、一流基础研究平台的建设和优秀人才的回国使得我国在这一领域硕果累累,相信在不久的将来我国的免疫检查点抑制剂将会走出国门,为全人类的癌症事业做出贡献．     

尼安德特人全基因组序列的测序历程——从中学生物学角度解读2022年诺贝尔生理学或医学奖

介绍了科学家斯万特·帕博在尼安德特人全基因组序列的测序过程中所作出的突出贡献,以及该历程体现的科学家精神,旨在为中学生物学教师介绍生物学前沿理论、扩充教学素材,开拓中学生的生物学视野,激发学生学习生物学的兴趣,为学生学习知识、从事科研活动提供榜样力量。     

An Expression Profile of Active Genes in Human Lung

An expression profile ofgenes active in the human lung was obtainedby collecting 797 partial sequences from a 3'-directed cDNAlibrary. Three genes were found to produce mRNA each of whichcomprised more than 1% of total mRNA. These three have beenidentified as genes for pulmonary surfactant apoprotein (PSP-A),Clara cells 10-kDa secretory protein, and HLA-E heavy chain.In the remaining 745 clones, 221 were composed of89 speciesthat occurred recurrently, and 524 clones appeared only once.Because the 3'-directed cDNA library faithfully represents themRNA population in the source tissue, these numbers representthe relative activities ofthe gene expression. Altogether 437gene species were novel, and 179 gene species were identifiedin GenBank. A significant portion ofthese genes encode proteinsfound in secretory proteins, cell surface proteins, and componentsin the protein synthesis machinery, representing the functionof the lung.     

An Expression Profile of Active Genes in Human Colonic Mucosa

An expression profile of genes active in the human colonic mucosawas obtained by collecting 959 partial sequences from a 3'-directedcDNA library. Seven genes were found to produce mRNA each ofwhich comprized more than 1% of total mRNA. Four of these genesare novel, and are likely to be uniquely expressed in the colonicmucosa, and the other three have been identified as genes forfatty acid binding protein, immunoglobulin lambda chain, andcarcinoma-associated antigen GA733-2. In the remaining 952 clones,310 were composed of 118 species occurred recurrently but lessthan 1%, and 533 clones appeared only once. Because the 3'-directedcDNA library faithfully represents the mRNA population in thesource tissue, these numbers represent the relative activitiesof the gene expression. Altogether 156 gene species were identified in GenBank, anda significant portion of these genes encode proteins found inGolgi apparatus and lysosomes, chromosome-encoded mitochondrialproteins, cell surface proteins, and components in the proteinsynthesis machinery. The types and proportions of genes identifiedis consistent with the known major activities of the colonicmucosa such as mucous protein production, energy-dependent waterabsorption, and rapid cell proliferation and turnover.     

Evolution of Hominin Detoxification: Neanderthal and Modern Human Ah Receptor Respond Similarly to TCDD

In studies of hominin adaptations to fire use, the role of the aryl hydrocarbon receptor (AHR) in the evolution of detoxification has been highlighted, including statements that the modern human AHR confers a significantly better capacity to deal with toxic smoke components than the Neanderthal AHR. To evaluate this, we compared the AHR-controlled induction of cytochrome P4501A1 (CYP1A1) mRNA in HeLa human cervix epithelial adenocarcinoma cells transfected with an Altai-Neanderthal or a modern human reference AHR expression construct, and exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). We compared the complete AHR mRNA sequences including the untranslated regions (UTRs), maintaining the original codon usage. We observe no significant difference in CYP1A1 induction by TCDD between Neanderthal and modern human AHR, whereas a 150–1,000 times difference was previously reported in a study of the AHR coding region optimized for mammalian codon usage and expressed in rat cells. Our study exemplifies that expression in a homologous cellular background is of major importance to determine (ancient) protein activity. The Neanderthal and modern human dose–response curves almost coincide, except for a slightly higher extrapolated maximum for the Neanderthal AHR, possibly caused by a 5′-UTR G-variant known from modern humans (rs7796976). Our results are strongly at odds with a major role of the modern human AHR in the evolution of hominin detoxification of smoke components and consistent with our previous study based on 18 relevant genes in addition to AHR, which concluded that efficient detoxification alleles are more dominant in ancient hominins, chimpanzees, and gorillas than in modern humans.     

Increased Expression of Several Mitochondrial Genes in Human and Monkey B-Cell Non-Hodgkin Lymphomas

Mitochondrial genes overexpressed in human and monkey B-cell non-Hodgkin lymphomas (B-NHLs) were sought via subtraction hybridization, cloning, and differential screening of the resulting cDNA libraries. The cDNAs of mitochondrial genes constituted an appreciable proportion of all lymphoma-specific cDNAs. Lymphomogenesis was associated with upregulation of a set of mitochondrial genes, which varied with lymphoma type but always included NADHIV. A possible association between upregulation of certain mitochondrial genes and cell malignant transformation is discussed.     

New Genes on Human Chromosome 7: Bioinformation Analysis of a Cluster of Genes from the POLR2J Family

Four independent genes encoding various variants of the hRPB11 subunit of Homo sapiens RNA polymerase II were revealed in human chromosome 7. Three genes (POLR2 J1, POLR2 J2, and POLR2 J3) form a cluster of total length of 214 530 bp in the genetic locus 7q22.1 on the long arm of chromosome 7 (contig NT_007933). The fourth gene (POLR2 J4, 31 040 bp) was localized in the cytogenetic locus 7p13 of the short arm of chromosome 7 (contig NT_007819). An analysis enabled us to refine dissimilar experimental data on the mapping of the hRPB11 subunit gene on chromosome 7. In particular, the presence of three sites of its localization according to data on hybridization with fluorescent-labeled probes (the FISH method) was explained. It was established that, upon the expression of the four human POLR2 J genes, at least 14 types of mature mRNAs encoding somewhat differing hRPB11 isoforms can be synthesized. Eleven of these mRNAs were revealed (as full-length copies or clearly identifiable fragments) in the available databases of expressed sequence tags and cDNAs. The most probable scheme of origination of the multiple genes of the POLR2 J family as a result of three consecutive segmented duplications increasing in size was proposed and substantiated. On the basis of the scheme, some assumptions on the pathways of evolution of separate human genes and the mechanisms of generation of protein diversity in higher eukaryotes were made.     

通过新基因计算机识别与实验确认对NCBI人类基因数据库一些模式参考序列错误的分析与纠正

采用生物信息学分析与实验确认相结合的技术路线,通过所识别的基因在非冗余数据库比对发现了网上公布的计算机注释人类基因组编码序列存在各种类型的多处错误,包括cDNA水平的一个或一段碱基插入、缺失或突变,或是这些错误的不同排列组合,其中以错误插入为多,往往导致编码氨基酸的移码突变。最先举证了NCBIGENOME Annotation Project预测人类新基因的下列错误类型：(1)开放读码框架(0RF)中错误插入一个碱基造成编码氨基酸移码;(2)错误拼接;(3)开放读框中错误插入一个或一段碱基造成该读框提前终止。只编码N-端氨基酸的cDNA序列而不完整;(4)只有编码c一端氨基酸序列的cDNA而不完整;(5)只是正确基因0RF中间的一段编码蛋白cDNA序列而不完整,缺N-端与C-端氨基酸序列,并且将不完整蛋白氨基酸序列的第一个非起始码氨基酸错误地预测为起始码氨基酸,如将L错误地预测为M;(6)开放读框中错误插入一个或一段碱基造成前面出现不该有的终止码,因而编码蛋白缺开头部分氨基酸;(7)可能将污染基因组序列当作完整基因cDNA序列对待而预测出所谓单一外显子基因。即便真是基因,也只是较长单一外显子mRNA中有一小0RF,而0RF起始码上游同一相位确实存在终止码,无其他特点符合基因条件;(8)所预测基因只有0RF,而0RF两端没有任何EST证据,可据此0RF拼接出受EST和人类基因组双重支持的完整基因cDNA(开放读框上游同一相位有终止码),预示所预测0RF参考序列可能不正确;(9)有EST实验证据支持存在基因的人类基因组序列范围内又被预测出一条相似但更小的蛋白编码基因,因而新预测基因有可能是错误的。     

Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia)

Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick‐billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray /sscape , soapdenovo 2 and platanus , in assembling the highly heterozygous genome of the thick‐billed murre. Our results show that platanus , an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick‐billed murre genome using a homology‐based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.     

Next-generation sequencing for identifying new genes in rare genetic diseases: many challenges and a pinch of luck

A report on the European Society of Human Genetics conference, held in Paris, France, June 8-11, 2013.