棘球属绦虫线粒体基因组全序列生物信息学分析

目的 利用生物信息学技术分析棘球属绦虫线粒体基因组全序列碱基组成、基因的结构组成及排列、蛋白基因核苷酸序列变异位点、密码子使用情况及偏好性、系统发育等,为研究棘球绦虫系统起源、演化、分类及亲缘关系等提供理论基础。方法 从GenBank数据库下载12种棘球属绦虫线mtDNA全序列,并以猪带绦虫作为外类群,构建系统发育树。利用OGDRAW在线分析网站及Vector NTI Express软件,分析mtDNA的组成及排列情况。用Clust-X软件对多个相似序列进行多重序列比对分析;使用Mega4.0软件选择邻接法构建进化树,并分析密码子使用情况;利用RNAfold在线预测网站使用minimum free energy (MFE) and partition function算法预测l-rRNA和s-rRNA二级结构。结果 除Eg G1外,棘球绦虫属mtDNA有36个编码基因,包括22个转运RNA基因、12个蛋白基因、2个核糖体RNA基因;但Eg G1 mtDNA最小,只有30个编码基因,在起始编码区缺少6个编码转运RNA的基因,且第一个编码基因不是ND5,而是COX3;编码蛋白的基因核苷酸序列变异率为27.9%~42.7%,其中COX1最为保守,ND5变异率最大达到42.7%;棘球属绦虫线粒体蛋白质编码基因起始密码子除atg,也有一些蛋白质以gtg作为起始密码子,终止密码子以taa和tag常见,但也有以ttt作为终止密码子的;棘球绦虫属使用的密码子为密码表9,使用频率最高的密码子是UUG(2.72%),频率最低的是CUC(1%)、CGC(1%),编码亮氨酸、精氨酸的密码子最多达6个,编码甲硫氨酸、色氨酸最少只有一个,亮氨酸也是棘球属绦虫最偏好的氨基酸达到6%;棘球属绦虫核糖体基因有两个长度大小分别为977~985 bp、700~727 bp,两个基因的位置十分靠近中间只隔一个trnC基因;系统进化树中Ev、Eo单独为一枝,Em、Es及Eg G1、Ef形成姐妹枝,细粒棘球绦虫G4、G5、G6、G7、G8、G10亚型聚为一枝,进化距离较近。结论 本研究将为棘球属绦虫mtDNA的研究、分子进化和分子诊断等方面提供诸多信息,并为种系鉴定起到一定的指导作用。     

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.     

人博卡病毒全基因组序列测定与种系分析

目的了解福州地区人博卡病毒(HBoV)在儿童呼吸道感染中的检出情况,并对其进行全基因组序列测定和种系分析。方法收集2007年11月至2008年10月在福建省妇幼保健院因下呼吸道感染住院的重症监护病房的57例小儿鼻咽抽取物标本,用一对特异引物通过PCR扩增法对HBoV基因片段进行检测,对检测出的2例HBoV(FZ1和FZ40)用7对全序列引物进行扩增和拼接,获得这两株病毒全基因组序列,上传GenBank并与基因库中国内外其它10株HBoV的全基因组序列和各氨基酸序列进行比对,并做种系分析。结果FZ1株基因组序列全长为5299bp,与HBoV参考株st2株序列长度相同;而FZ40株的基因组序列全长少2bp。病毒全基因组编码4种蛋白,分别是非结构蛋白NS1、核蛋白NP-1和衣壳蛋白VP1、VP2。结论种系分析显示福州的FZ40株与浙江温岭的WLL-1株关系较近,而FZ1株与北京的两株及泰国的CU6株关系较近。     

中国卫氏并殖吸虫线粒体基因组及多地域株的系统发育分析

目的　对福建省大、小囊蚴来源的两型卫氏并殖吸虫线粒体基因组序列进行比较和系统发育分析，探寻其可能存在的与表型相关的遗传特征。方法　以在福建省南平市延平区太平镇溪蟹中分离出的两种大小不同的囊蚴（直径分别为380～420 μm和320～340 μm）分别感染犬，收集犬粪及肺部虫卵及成虫。比较两种来源虫卵大小及外形差异；抽提两型并殖吸虫成虫基因组DNA，扩增并获得线粒体全基因组序列，进行序列结构及系统发育关系分析。结果　大、小囊蚴分别感染犬后，所获得的成虫体肥厚，具口、腹吸盘，腹吸盘位于体中线稍前，可见睾丸、卵巢和卵黄腺等结构，固定后呈椭圆形，长宽比约为1.7∶1。两组卵在长、宽上均有显著性差异，大囊蚴感染后所获虫卵亦较大。两组成虫和卵形态特征及ITS2基因序列符合卫氏并殖吸虫特征。成虫线粒体基因组序列分析显示，大、小囊蚴来源的成虫线粒体基因组蛋白编码区序列基本一致，主要差异区域位于前非编码区。滑动窗口分析显示，不同地域来源的卫氏并殖吸虫线粒体基因组间，多态性最大区域位于ND4基因内。系统发育分析表明，两型并殖吸虫均聚入卫氏并殖吸虫中国地域分支，与韩国/日本株关系较近，与（东）南亚株遗传距离较远。结论　中国福建大、小囊蚴来源的两型卫氏并殖吸虫在线粒体基因组水平上遗传距离较近，未表现出明显分化，但非编码区突变和结构变化可能影响了两者在表型上的差异。此外，线粒体各编码基因的进化速率存在明显差异，提示在进行系统发育等相关研究时，应注意选择合适的分子标记。     

血吸虫病肝纤维化小鼠IL-22表达及肝星状细胞衰老的意义

目的 目的 观察血吸虫病肝纤维化小鼠模型中白介素22 （IL?22） 及其受体 （IL?22R1） 的表达状况, 并对与IL?22相关的 肝星状细胞 （HSC） 衰老机制进行探讨。方法 方法 建立血吸虫病肝纤维化小鼠模型, 按感染后第4、 6、 8周及12周时间点取材, 行生化功能检测、 HE染色和Masson染色、 β?半乳糖苷酶染色检测HSC衰老状况、 ELISA检测肝组织中IL?22蛋白水平、 荧光 定量PCR检测肝组织中IL?22及IL?22R1mRNA表达水平, 另设未感染小鼠为对照组。结果 结果 感染后第8、 12周时血清中丙 氨酸氨基转移酶和天冬氨酸氨基转移酶水平较对照组明显增高 （P均＜0.05）。肝组织中IL?22蛋白于感染后第4、 6周时表 达较对照组明显增加 （P均＜0.05）, 感染后第8周时, 其表达水平较前下降, 第12周时仍维持在较低水平, 较第4、 6周差异 均有统计学意义 （P均＜0.01）。IL?22mRNA动态变化与蛋白水平一致, 感染后第4周时表达升高, 第6周时达高峰, 与对照 组比较差异均有统计学意义 （P均＜0.05）, 第8、 12周表达持续下降, 较第 6周差异均有统计学意义 （P均＜0.05）。IL? 22R1mRNA表达随病程进展逐渐升高, 于12周时达高峰, 较对照组、 第6周差异均有统计学意义 （P均＜0.05）。检测发现 HSC衰老, 随着IL?22在晚期病程中下降, HSC衰老减少。结论 结论 IL?22及其受体参与血吸虫病肝纤维化病程进展, 早期作 为炎症因子之一, 参与炎症反应; 至肝纤维化病程后期, 可部分通过诱导HSC衰老, 限制肝纤维化发展。     

Mitigation of age-dependent accumulation of defective mitochondrial genomes

Unknown processes promote the accumulation of mitochondrial DNA (mtDNA) mutations during aging. Accumulation of defective mitochondrial genomes is thought to promote the progression of heteroplasmic mitochondrial diseases and degenerative changes with natural aging. We used a heteroplasmic Drosophila model to test 1) whether purifying selection acts to limit the abundance of deleterious mutations during development and aging, 2) whether quality control pathways contribute to purifying selection, 3) whether activation of quality control can mitigate accumulation of deleterious mutations, and 4) whether improved quality control improves health span. We show that purifying selection operates during development and growth but is ineffective during aging. Genetic manipulations suggest that a quality control process known to enforce purifying selection during oogenesis also suppresses accumulation of a deleterious mutation during growth and development. Flies with nuclear genotypes that enhance purifying selection sustained higher genome quality, retained more vigorous climbing activity, and lost fewer dopaminergic neurons. A pharmacological agent thought to enhance quality control produced similar benefits. Importantly, similar pharmacological treatment of aged mice reversed age-associated accumulation of a deleterious mtDNA mutation. Our findings reveal dynamic maintenance of mitochondrial genome fitness and reduction in the effectiveness of purifying selection during life. Importantly, we describe interventions that mitigate and even reverse age-associated genome degeneration in flies and in mice. Furthermore, mitigation of genome degeneration improved well-being in a Drosophila model of heteroplasmic mitochondrial disease.

Unlike nuclear genotype, which is largely stable during one’s lifetime, when genetically distinct mitochondrial genomes co-reside (heteroplasmy), their relative proportions shift during growth, development, and aging. This shift is not random (1–7). Mutant mitochondrial DNA (mtDNA) variants accumulate during aging and in the progression of some mitochondrial diseases (1–5). Stereotyped changes in abundance of particular alleles in different tissues in human and mouse indicate that selective forces favor different mitochondrial genomes (3, 6, 7). However, despite the importance of mitochondrial function to health and well-being, we have limited understanding of the processes underlying the accumulation of mitochondrial mutations with age.The nuclear genome encodes mechanisms of quality control that survey the function of mitochondria and eliminate or compromise the proliferation of defective mitochondria (8, 9). Two described mechanisms use PINK1, the product of a gene discovered as one of the causes of early-onset familial Parkinson’s disease, as a sensor of mitochondrial function. PINK1 accumulates on the surface of mitochondria having a reduced membrane potential, and its kinase activity in this location signals several downstream events (10–15). In one pathway defined largely in a cell culture model, PINK1 activates PARKIN, the product of another Parkinson’s disease gene, which then triggers elimination of compromised mitochondria by mitophagy (16). In a second pathway, acting in the Drosophila female germ line (17, 18), PINK1 acts in a PARKIN-independent pathway that targets a protein called Larp to inhibit its role in promoting biogenesis of the mitochondria (18) (SI Appendix, Fig. S2).Since deleterious mtDNA mutations compromise electron transport of mitochondria, it seems that quality control would put genomes carrying such mutations at a disadvantage, creating a purifying selection that leads to their elimination. However, this outcome is far from certain. Various factors such as the sharing of gene products among mitochondria as a result of dynamic fission and fusion could mask the consequences of heteroplasmic mutations, shielding them from quality control. Indeed, a number of studies suggest a contrast between the germ line, which exhibits purifying selection, and adult somatic tissues, which often show accumulation of mutations. Studies in Drosophila show that purifying selection acting in the female germ line eliminates deleterious mutations in a few generations (18–21). Genetic dissection revealed that this purifying selection depends on the PINK1/LARP pathway of quality control (18). On the other hand, an elegant study that induced heteroplasmic deletions in the flight muscle of the adult fly detected no substantial indications of purifying selection unless additional stressors were introduced (22). Furthermore, a detailed study in Drosophila carrying a proofreading defective mitochondrial DNA polymerase (mutator line) showed that adult flies accumulate a spectrum of mutations biased toward deleterious mutations (23). Since deleterious mutations would potentially be removed by purifying selection, this finding argues either that it was not operating or that it was opposed by a stronger selection favoring deleterious mutations (23). Similarly, studies in mouse suggest a discordance between germ line and soma. When mutations in the mitochondrial genome that were introduced in a mutator line were passed through subsequent generations in a wild-type background, there was selective elimination of deleterious mutations, a strong signal of purifying selection (7). In contrast, zygotically accumulated mutations in the mutator mouse exhibited high levels of deleterious mutations, suggesting a lack of purifying selection in the soma. Furthermore, Parkin mutant mice did not show a significant increase in mutations in adult wild-type or mutator mice, suggesting that Parkin-dependent quality control does not contribute to purifying selection (16). While these studies suggest major changes in the efficiency of purifying selection, other studies have suggested continued purifying selection in some circumstances. For example, adult human T cells of mitochondrial disease patients show exceptionally low heteroplasmy levels, suggesting cell type-specific action of purifying selection (24). We sought to measure purifying selection and to understand the nature of quality control in the soma during growth, development, and aging using an experimental model developed in Drosophila.A previously described heteroplasmic line of Drosophila melanogaster carries a wild-type mitochondrial genome (Yak-mt) from another species, Drosophila yakuba, and a D. melanogaster genome (Mel-mt^ts) crippled by a temperature-sensitive mutation in cytochrome oxidase subunit 1 (mt:CoI^T300I) [Fig. 1A and (25)]. The Mel-mt^ts genome has an intrinsic advantage in replication. At a permissive temperature, it gradually displaces the Yak-mt genome, resulting in the loss of the D. yakuba genome in a few generations (25). At 29 °C, a temperature at which the CoI^T3000I mutant cannot support viability (26), purifying selection counters the replicative advantage of the mutant Mel-mt^ts genome, preventing it from taking over (25). qPCR gives a measure of the ratio Yak-mt/total-mt. The difference in this ratio between permissive and restrictive temperatures allows us to assess the impact of a functional disparity on competition between the two genomes and provides a measure of purifying selection.Open in a separate windowFig. 1.Quality control modulates the ratio of heteroplasmic mitochondrial genomes during development. (A) Heteroplasmy for schematized Yak-mt and Mel-mt^ts genomes was established by transferring cytoplasm of D. yakuba embryos into D. melanogaster embryos carrying the doubly mutant genome mt:ND2^del + mt:Col^T300I (Mel-mt^ts). (B) The proportion of Yak-mt (Yak-mt/total-mt) following development from egg to adult shows action of quality control. Eggs (2-h collection at 29 °C) were assayed (gray bar) or allowed to develop to 5 d after eclosion at 22 °C (blue) or 29 °C (amber). Adult females have a large contribution from oocyte mtDNA. (C) Quality control operates in multiple tissues with different effectiveness. The blue and amber bars (22 °C or 29 °C, respectively) show the proportion of Yak-mt in different tissues of late third instar larvae. (D) The impact of purifying selection declined with age in the CNS. (E) The decline in relative abundance of wild-type, indicated by the dashed regression lines (orange for 29°C and blue for 22°C), Yak-mt following eclosion was fast. (F) The signature of quality control is absent during maturation of adults. Yak-mt/total-mt ratios from gut and brain taken from 5-d (gray bars) or 20-d adults aged at 22 °C or 29 °C (blue and amber bars, respectively). Here and below, *P < 0.05; **P < 0.01; and ***P < 0.001 by one-way ANOVA/Tukey’s multiple comparison test. Data represent eight independent biological repeats, with each repeat being an average of ratios assessed in three samples of eggs or adults. For tissues, data represent tissues dissected from eight individuals. Error bars represent standard error. In E, slopes differ (*P < 0.05) by linear regression. Cyto, cytoplasm; AED, after egg deposition; ns, not significant.Past work using this heteroplasmic line focused on changes in the relative abundance of the two genomes from one generation to the next and uncovered the action of purifying selection during oogenesis (18–21, 25, 27). It is notable that this selection depends on quality control, occurs by competition between mitochondria within the oocyte, and does not involve selection for organismal fitness (18, 21). Changes in the ratio of Yak-mt/total-mt during the lifetime of the fly suggested that maintenance of this ratio is dynamic (25). Here, we examined changes in the relative abundance of the two genomes in the soma. Shifts in the ratio of Yak-mt/total-mt provide a measure of the effectiveness of purifying selection during the life of the fly and a means of assessing whether purifying selection can be genetically or pharmacologically modified. We found evidence that purifying selection is active in the soma during growth and development. The influence of mutations in quality control genes suggests that somatic mechanisms of quality control overlap those operating in the germ line. However, the effectiveness of purifying selection declines with age and has no obvious impact in tested tissues beyond 5 d after eclosion of adult flies. Importantly, we found that quality control can be stimulated in the adult by genetic alterations or by feeding kinetin and that such measures forestall mutational accumulation and aging phenotypes in Drosophila and can reverse mutational accumulation in aged mice.     

Revising the recent evolutionary history of equids using ancient DNA

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87–688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.     

福建省登革1型病毒基因组序列测定及进化分析

目的对分离自福建省的1株登革1型病毒（FJ231／04）进行全基因组序列测定，并同其它病毒株全基因序列进行比较，了解其序列特征和可能的传播来源。方法采取分段扩增、克隆、测序的方案，设计10对引物分别扩增不同的片段，基因组5’末端序列采用RACE技术进行扩增，扩增产物随后克隆到质粒载体并测序。通过末端重叠序列进行拼按后组成全长病毒基因组序列。结果拼接后的病毒全基因组全长10735nt，编码一个长的开放读码框。参考已公布的登革1型病毒的全基因序列，对该病毒株进行进化分析。序列的进化分析表明，该福建省分离株属登革1型病毒中的第1群（基因1型）病毒。在遗传距离上，该毒株和2002年的泰国分离株最为接近（差异为0．53％）。根据病毒发现时间及其核酸差异，推测该病毒可能是通过在东南亚一带感染者或病人带入福建。结论通过对登革病毒金基因组序列的测定可以获得毒株的特征。此外病毒序列的进化分析，还可为了解病毒可能的来源以及传播途径，正确了解登革病毒在我省的流行病学概况提供重要的线索。     

Complete mitochondrial DNA genome sequences from the first New Zealanders

The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.     

Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes

Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling >5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome.     

绒螨目线粒体基因组研究进展

绒螨目是一个数量庞大且分散的类群,许多绒螨目螨类具有医学和经济学意义。本文从线粒体基因组的一般结构及基因重排、蛋白质编码基因、rRNA基因、tRNA基因、控制区、系统发育关系六个方面对绒螨目螨类线粒体基因组进行回顾,综述了当前已测序的绒螨目螨类线粒体基因组,系统总结了近年来报道的绒螨目线粒体全序列的基因特征、绒螨目的系统发育关系。     

钉螺线粒体基因组DNA提取方法的优化及比较

目的优化提取钉螺线粒体基因组DNA(mt DNA)的方法。方法应用高温裂解、蛋白酶K变温消化和醋酸钾纯化对传统的高盐沉淀法进行优化,并将优化的高盐沉淀法与蔗糖密度梯度离心法、传统的高盐沉淀法进行比较。用紫外分光光度计、琼脂糖凝胶电泳和线粒体COX1基因PCR扩增产物鉴定提取的mt DNA,并用核ITS基因PCR扩增产物检测有无核DNA污染。结果优化的高盐沉淀法获得的mt DNA浓度和产量较高,差异有统计学意义(F=3 032.65、10185.00,P均0.01)。用凝胶电泳检测后未发现核DNA与蛋白质污染,质量可满足于PCR、测序等分子生物学研究。结论优化的高盐沉淀法简易高效,成本低,获得的mt DNA能满足相关分析要求。     

两株犬源狂犬病病毒街毒株全基因组序列测定与分析

目的对2株犬源狂犬病病毒街毒株全基因组测序,了解国内狂犬病病毒的流行和变异情况。方法采用乳鼠脑内接种方法分离2株天津地区狂犬病病毒街毒株,RT-PCR扩增病毒DNA覆盖全基因组12个相互重叠的基因片段,PCR产物平端克隆后进行全基因组核苷酸序列测定,然后对其分子变异和进化特点进行分析。进行两分离株的序列相似性、氨基酸同源性、主要功能位点的变异比较和种系发生分析。结果 TJD04和TJD05两株狂犬病病毒全基因组长均为11 924 nts,全基因组序列的组成和结构均符合弹状病毒科狂犬病病毒属的特征。病毒基因组由5个编码区组成,基因起始位点和终止位点高度保守,氨基酸编码长度未发生变异,5个编码蛋白序列较少发生变化,仅有个别主要功能位点发生变异,且大部分变异均属于无意义沉默突变。多序列相似性比较和种系发生分析显示,两株病毒均属于基因1型,N基因与全基因进化树保持一致,与中国犬源狂犬病病毒BD06同源性最高(99.6%),进化关系近,并具有较为独特的中国地域特点。结论两天津株狂犬病毒可能是自然界中固有的狂犬病病毒街毒株。     

Genomic analysis of multiple myeloma using targeted capture sequencing in the Japanese cohort

Previous genomic studies have revealed the genomic landscape of myeloma cells. Although some of the genomic abnormalities shown are believed to be correlated to the molecular pathogenesis of multiple myeloma and/or clinical outcome, these correlations are not fully understood. The aim of this study is to elucidate the correlation between genomic abnormalities and clinical characteristics by targeted capture sequencing in the Japanese multiple myeloma cohort. We analysed 154 patients with newly diagnosed multiple myeloma. The analysis revealed that the study cohort consisted of a less frequent hyperdiploid subtype (37·0%) with relatively high frequencies of KRAS mutation (36·4%) and IGH-CCND1 translocation (26·6%) compared with previous reports. Moreover, our targeted capture sequencing strategy was able to detect rare IGH-associated chromosomal translocations, such as IGH-CCND2 and IGH-MAFA. Interestingly, all 10 patients harboured MAX mutations accompanied by 14q23 deletion. The patients with del(17p) exhibited an unfavourable clinical outcome, and the presence of KRAS mutation was associated with shorter survival in patients with multiple myeloma, harbouring IGH-CCND1. Thus, our study provides a detailed landscape of genomic abnormalities, which may have potential clinical application for patients with multiple myeloma.     

Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet

Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.     

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases, State of Washington v Anthony Eugene Whitfield, case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and State of Texas v Philippe Padieu, case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant.