Karyotypic evolution in family Hipposideridae (Chiroptera, Mammalia) revealed by comparative chromosome painting, G- and C-banding

Comparing to its sister-family （Rhinolophidae）, Hipposideridae was less studied by cytogenetic approaches. Only a few high-resolution G-banded karyotypes have been reported so far, and most of the conclusions on the karyotypic evolution in Hipposideridae were based on conventional Giemsa-staining. In this study, we applied comparative chromosome painting, a method of choice for genome-wide comparison at the molecular level, and G- and C-banding to establish comparative map between five hipposiderid species from China, using a whole set of chromosome-specific painting probes from one of them （Aselliscus stoliczkanus）. G-band and C-band comparisons between homologous segments defined by chromosome painting revealed that Robertsonian translocations, paracentric inversions and heterochromatin addition could be the main mechanism of chromosome evolution in Hipposideridae. Comparative analysis of the conserved chromosomal segments among five hipposiderid species and outgroup species suggests that bi-armed chromosomes should be included into the ancestral karyotype of Hipposideridae, which was previously believed to be exclusively composed of acrocentric chromosomes.

Characterization of Two Human Lung Adenocarcinoma Cell Lines by Reciprocal Chromosome Painting

Lung cancer is a leading cause of cancer death worldwide. Some lung cancer patients correlate with a gas of radon besides smoking. To search for common chromosomal aberrations in lung cancer cell lines established from patients induced by different factors, a combined approach of chromosome sorting, forward and reverse chromosome painting was used to characterize karyotypes of two lung adenocarcinoma cell lines： A549 and GLC-82 with the latter line derived from a patient who has suffered long-term exposure to environmental radon gas pollution. The chromosome painting results revealed that complex chromosomal rearrangements occurred in these two lung adenocarcinoma cell lines. Thirteen and twenty-four abnormal chromosomes were identified An A549 and GLC-82 cell lines, respectively. Almost half of abnormal chromosomes in these two cell lines were formed by non-reciprocal translocations, the others were derived from deletions and duplication/or amplification in some chromosomal regions. Furthermore, two apparently common breakpoints, HSA8q24 and 12q14 were found in these two lung cancer cell lines.

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.

鹿科麂属动物基因组演化研究进展

鹿科麂属(Muntiacus,Cervidae)在近两三百万年内经历了快速物种辐射,但其物种间核型差异大.5个现生种核型数显示,该类染色体数目范围从小麂(Muntiacus reevesi)的46条到赤麂(M.muntjak vaginalis)的6条.该类的因组在较短时间内发生了快速演化,使其成为进化生物学研究的理想材料.40多年来,技的革新使该领域的研究不断深入,染色体重排的类型、推动重排的分子制及物种间的核型演化历程逐渐被阐释.而且,研究中发现,雄性黑麂(M.crinifrons)1p+4染色体的演化途径与哺乳动物Y染色体的演化历程相似,可成为哺乳动物性染色体演化研究的珍贵模型.有关麂动物因组演化依有许多问题等待更加全面、深入的探讨.本文总结了该领域研究进展,并对未来研究热点进行了展望.

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.

Dev Cell:科学家阐明人类胚胎原生殖细胞发育的分子机制

近日,刊登于国际杂志Developmental Cell上的一项研究报道中，来自巴布拉汉研究所（Babraham Insdtute）的研究人员通过研究调查了原生殖细胞发育的早期阶段，同时他们在实验室开发了一种产生类似细胞的策略，这种酷似人类原始生殖细胞的产生对于未来生殖领域的研究，以及分析人类潜在的继代基因调控的遗传机制非常重要。

PNAS:维生素A和C如何擦除细胞记忆?

维生素A和C不只是对我们的健康有益，其还会影响到机体的DNA，日前一项刊登于国际杂志PNAS上的研究论文中，来自巴布拉汉研究所（Babraham Institute）等机构的研究人员通过研究揭示了维生素A和C如何修饰细胞的表观遗传记忆。相关研究或为后期研究者们开发新型再生医学疗法或者对细胞重编程提供一定的思路。

Molecular markers for artemisinin and partner drug resistance in natural Plasmodium falciparum populations following increased insecticide treated net coverage along the slope of mount Cameroon:cross-sectional study

Background:Drug resistance is one of the greatest challenges of malaria control programmes,with the monitoring of parasite resistance to artemisinins or to Artemisinin Combination Therapy(ACT)partner drugs critical to elimination efforts.Markers of resistance to a wide panel of antimalarials were assessed in natural parasite populations from southwestern Cameroon.Methods:Individuals with asymptomatic parasitaemia or uncomplicated malaria were enrolled through crosssectional surveys from May 2013 to March 2014 along the slope of mount Cameroon.Plasmodium falciparum malaria parasitaemic blood,screened by light microscopy,was depleted of leucocytes using CF11 cellulose columns and the parasite genotype ascertained by sequencing on the Illumina HiSeq platform.Results:A total of 259 participants were enrolled in this study from three different altitudes.While some alleles associated with drug resistance in pfdhfr,pfmdr1 and pfcrt were highly prevalent,less than 3%of all samples carried mutations in the pfkelch13 gene,none of which were amongst those associated with slow artemisinin parasite clearance rates in Southeast Asia.The most prevalent haplotypes were triple mutants PfdhfrI51R59N108I164(99%),pfcrt-C72V73I74E75T76(47.3%),and single mutants PfdhpsS_(436)G_(437)K_(540)A_(581)A_(613)(69%)and Pfmdr1 N_(86)F)(184)D_(1246)(53.2%).Conclusions:The predominance of the Pf pfcrt CVIET and Pf dhfr IRN triple mutant parasites and absence of pfkelch13 resistance alleles suggest that the amodiaquine and pyrimethamine components of AS-AQ and SP may no longer be effective in their role while chloroquine resistance still persists in southwestern Cameroon.

aunalysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Dear Editor Salvia miltiorrhiza Bunge （Danshen） is a medicinal plant of the Lamiaceae family, and its dried roots have long been used in traditional Chinese medicine with hydrophilic phenolic acids and tanshinones as pharmaceutically active components （Zhang et al., 2014; Xu et al., 2016）. The first step of tanshinone biosynthesis is bicyclization of the general diterpene precursor （E,E,E）-geranylgeranyl diphosphate （GGPP） to copalyl diphosphate （CPP） by CPP synthases （CPSs）, which is followed by a cyclization or rearrangement reaction catalyzed by kaurene synthase-like enzymes （KSL）. The resulting intermediate is usually an olefin, which requires the insertion of oxygen by cytochrome P450 mono-oxygenases （CYPs） for the final production of diterpenoids （Zi et al., 2014）. While the CPS, KSL, and several early acting CYPs （CYP76AH1, CYP76AH3, and CYP76AK1） for tanshinone biosynthesis have been identified in S. miltiorrhiza （Gao et al., 2009; Guo et al., 2013, 2016; Zi and Peters, 2013）, the majority of the overall biosynthetic pathway, as well as the relevant regulatory factors associated with tanshinone production, remains elusive （Figure 1B）.

Pluripotency and its layers of complexity

Pluripotency is depicted by a self-renewing state that can competently differentiate to form the three germ layers.Different stages of early murine development can be captured on a petri dish,delineating a spectrum of pluripotent states,ranging from embryonic stem cells,embryonic germ cells to epiblast stem cells.Anomalous cell populations displaying signs of pluripotency have also been uncovered,from the isolation of embryonic carcinoma cells to the derivation of induced pluripotent stem cells.Gaining insight into the molecular circuitry within these cell types enlightens us about the significance and contribution of each stage,hence deepening our understanding of vertebrate development.In this review,we aim to describe experimental milestones that led to the understanding of embryonic development and the conception of pluripotency.We also discuss attempts at exploring the realm of pluripotency with the identification of pluripotent stem cells within mouse teratocarcinomas and embryos,and the generation of pluripotent cells through nuclear reprogramming.In conclusion,we illustrate pluripotent cells derived from other organisms,including human derivatives,and describe current paradigms in the comprehension of human pluripotency.

Using mouse models to study function of transcriptional factors in T cell development

Laboratory mice have widely been used as tools for basic biological research and models for studying human diseases.With the advances of genetic engineering and conditional knockout(CKO)mice,we now understand hematopoiesis is a dynamic stepwise process starting from hematopoietic stem cells(HSCs)which are responsible for replenishing all blood cells.Transcriptional factors play important role in hematopoiesis.In this review we compile several studies on using genetic modified mice and humanized mice to study function of transcriptional factors in lymphopoiesis,including T lymphocyte and Natural killer(NK)cell development.Finally,we focused on the key transcriptional factor Bcl11b and its function in regulating T cell specification and commitment.

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.

Delineating nuclear reprogramming

Nuclear reprogramming is described as a molecular switch,triggered by the conversion of one cell type to another.Several key experiments in the past century have provided insight into the field of nuclear repro-gramming.Previously deemed impossible,this re-search area is now brimming with new findings and developments.In this review,we aim to give a historical perspective on how the notion of nuclear reprogram-ming was established,describing main experiments that were performed,including(1)somatic cell nuclear transfer,(2)exposure to cell extracts and cell fusion,and(3)transcription factor induced lineage switch.Ultimately,we focus on(4)transcription factor induced pluripotency,as initiated by a landmark discovery in 2006,where the process of converting somatic cells to a pluripotent state was narrowed down to four tran-scription factors.The conception that somatic cells possess the capacity to revert to an immature status brings about huge clinical implications including per-sonalized therapy,drug screening and disease model-ing.Although this technology has potential to revolu-tionize the medical field,it is still impeded by technical and biological obstacles.This review describes the effervescent changes in this field,addresses bottle-necks hindering its advancement and in conclusion,applies the latest findings to overcome these issues.

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。