The Identification of a Novel, High Frequency Variant in the Cytochrome b Gene in an Isolated Population of a Rare Fish, Spined Loach <i>Cobitis taenia</i>, in England: A Population Worth Protecting?

The spined loach Cobitis taenia, is listed as a protected species under Appendix 3 of the Bern Convention and Annex II of the European Council Directive (92/43/EEC) on the conservation of natural habitats and of wild fauna and flora. It is desirable therefore to understand the genetic diversity within European populations. In a molecular genetic analysis of the cytochrome b gene in Cobitis taenia from three sites in the upper reaches of the River Trent catchment, a novel high frequency variant was identified which has not been previously reported in any European or Non-European population.

Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS)

Comprehensive identification of conditionally essential genes requires efficient tools for generating high-density transposon libraries that, ideally, can be analysed using next-generation sequencing methods such as Transposon Directed Insertion-site Sequencing (TraDIS). The Himar1 (mariner) transposon is ideal for generating near-saturating mutant libraries, especially in AT-rich chromosomes, as the requirement for integration is a TA dinucleotide, and this transposon has been used for mutagenesis of a wide variety of bacteria. However, plasmids for mariner delivery do not necessarily work well in all bacteria. In particular, there are limited tools for functional genomic analysis of Pasteurellaceae species of major veterinary importance, such as swine and cattle pathogens, Actinobacillus pleuropneumoniae and Pasteurella multocida, respectively. Here, we developed plasmids, pTsodCPC9 and pTlacPC9 (differing only in the promoter driving expression of the transposase gene), that allow delivery of mariner into both these pathogens, but which should also be applicable to a wider range of bacteria. Using the pTlacPC9 vector, we have generated, for the first time, saturating mariner mutant libraries in both A. pleuropneumoniae and P. multocida that showed a near random distribution of insertions around the respective chromosomes as detected by TraDIS. A preliminary screen of 5000 mutants each identified 8 and 14 genes, respectively, that are required for growth under anaerobic conditions. Future high-throughput screening of the generated libraries will facilitate identification of mutants required for growth under different conditions, including in vivo, highlighting key virulence factors and pathways that can be exploited for development of novel therapeutics and vaccines.

利用piggyBac载体制备小鼠诱导性多能干细胞

小鼠体细胞可通过转入干细胞转录因子而诱导生成多能干细胞,这种干细胞称为诱导性多能干细胞(iPSC).利用逆转录病毒、慢病毒、腺病毒、质粒载体、多蛋白表达系统、合成性mRNA及microRNA已成功将小鼠和人的体细胞诱导成多能干细胞.piggyBac是转座频率较高的转座子载体,也已作为载体成功诱导出多能干细胞.为了研究以piggyBac载体诱导出的多能干细胞的体内外分化能力,利用携带Oct4,Sox2,Klf4和c-Myc转录因子的piggyBac转座载体进行了小鼠体细胞的转染诱导,结果诱导获得的iPS细胞碱性磷酸酶染色呈阳性;免疫组化染色OCT4,NANOG,SSEA-1为阳性;RT-PCR检测Oct4,Sox2,c-Myc和Klf4呈阳性.同时诱导获得的iPS细胞系在体外自发分化后,免疫组化染色AFP,BRACHYURY和NCAM1呈阳性,表明分化形成了3个胚层的细胞;该细胞系皮下注射免疫缺陷小鼠iPS细胞形成了畸胎瘤.实验发现,获得的干细胞系可与小鼠8-细胞聚合,进入到嵌合胚胎的内细胞团.这些结果表明,由piggyBac载体诱导的小鼠多能干细胞iPS具有干细胞的主要特性,包括体内外的分化能力.

利用piggyBac转座子制备牛成体多能干细胞诱导技术研究

通过逆转录病毒等媒介表达核转录因子Oct4、Sox2、Klf4、c-Myc可将体细胞重编程为诱导多能干细胞(induced pluripotent stem cells,iPSc)。时至今日,已经报道了小鼠、人、大鼠、猪、羊、马、牛的iPS细胞,但大动物iPS的多能性特别是嵌合体形成和生殖细胞传代还没有得到确认。与逆转录病毒等不同的是,piggyBac转座子转染效率高且无病毒源性、操作简单,可以在转座酶的存在下被安全切除。首次尝试了采用piggyBac转座子携带鼠源Oct4、Sox2、Klf4、c-Myc、Rarg和Lrh1 6个核转录因子诱导胎牛成纤维细胞,成功获得牛类iPS细胞,其形态与小鼠胚胎干细胞相似,克隆边界清晰、呈丘状、克隆内细胞致密、核大。RT-PCR与免疫组织化学染色分析均显示牛类iPS细胞表达多能性基因。该类细胞体外诱导分化可形成类胚体EB,且表达3个胚层的基因;体内诱导分化可形成畸胎瘤,苏木精、伊红染色显示瘤体有三胚层的分化。上述结果显示利用piggyBac转座子制备牛多潜能干细胞诱导技术可行,产生的牛类iPS细胞具有潜在多能性。

Oxford Nanopore MinION Sequencing and Genome Assembly

The revolution of genome sequencing is continuing after the successful secondgeneration sequencing （SGS） technology. The third-generation sequencing （TGS） technology, led by Pacific Biosciences （PacBio）, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies （ONT）. MiniON identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MiniON has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assem- bly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

How Often Does Human DNA Mutate?

Editor＇s comments The human mutation rate how often new changes appear in the DNA--is fundamental to understanding many aspects of medical genetics and human evolutionary genetics. But it is low, and has therefore been difficult to measure. In the past, scientists could only estimate it approximately, either by observing how often mutant phenotypes appeared, or by comparison of humans and closely related species, such as chimpanzee, where many mutations could accumulate but the time period was uncertain. Now, a new study supported by the NSFC in China and The Royal Society in the UK reports the first direct measurement of the human mutation rate at the individual letters （ nucleotides or bases） of DNA. This was possible because new （ next ）-generation sequencing technology is much more powerful than the methods available previously. The work was published in the lead- ing journal Currerzt Biology on 15th September 2009. The results were reported in the news by Nature, Science and the BBC , as well as in more than 20 Chinese newspapers and radio stations after the work first appeared online on 27th August. It was also one of the research highlights in Nature on 3rd September, which commented ＂ This direct measurement of the human mutation rate should help researchers to refine evolutionary dating and better understand the source of genetic disease＇. From the work, researchers could estimate that everyone has around 200 new mutations in their genome ; as the authors said, ＂we are all mutants＂. The ability to reliably measure rates of DNA mutation means we can begin to ask how mutation rates vary between different regions of the genome and perhaps also between different individuals.

Comprehensive Analysis of Pan-African Mitochondrial DNA Variation Provides New Insights into Continental Variation and Demography

Africa is the cradle of all human beings, and although it has been the focus of a number of genetic studies, there are many questions that remain unresolved. We have performed one of the largest and most comprehensive meta-analyses of mitochondrial DNA （mtDNA） lineages carried out in the African continent to date. We generated high-throughput mtDNA single nucleotide polymorphism （SNP） data （230 SNPs） from 2024 Africans, where more than 500 of them were additionally genotyped for the control region. These data were analyzed together with over 12,700 control region profiles collected from the literature, representing more than 300 population samples from Africa. Insights into the African homeland of humans are discussed. Phylogeographic patterns for the African continent are shown at a high phylogeographic resolution as well as at the population and regional levels. The deepest branch of the mtDNA tree, haplogroup L0, shows the highest sub-haplogroup diversity in Southeast and East Africa, suggesting this region as the homeland for modem humans. Several demographic estimates point to the coast as a facilitator of human migration in Africa, but the data indicate complex patterns, perhaps mirroring the effect of recent continental-scaled demographic events in re-shaping African mtDNA variability.

Nat Genet:科学家设计新方法找到抑制癌症发育的新基因

英国桑格研究院的研究人员和他们的合作者们最近发现了帮助阻止前列腺癌、皮肤癌和乳腺癌发育的新基因。这些基因能够与众所周知的肿瘤抑制基因PTEN配合发挥作用，该研究还发现这些基因与人类前列腺肿瘤存在相关性。相关研究结果发表在国际学术期刊Nature Genetics上。该研究揭示了一些参与癌症发育的新途径，这些基因有望成为治疗PTEN突变癌症的新药物靶点。这项研究开发的一些方法也可以用于发现其他协同抑制癌症生长的基因。