230 resultados para ECTOPIC RECOMBINATION
Resumo:
The femtosecond pump-probe technique was used to study the carrier dynamics of amorphous Ge2Sb2Te5 films. With carrier density at around 10(20)-10(21) cm(-3), carriers were excited within 1 ps and recovered to the initial state for less than 3 ns. On the picosecond time scale, the carrier relaxation consists of two components: a fast process within 5 ps and a slow process after 5 ps. The relaxation time of the fast component is a function of carrier density, which increases from 1.9 to 4.3 ps for the carrier density changing from 9.7x10(20) cm(-3) to 3.1x10(21) cm(-3). A possible interpretation of the relaxation processes is elucidated. In the first 5 ps the relaxation process is dominated by an intraband carrier relaxation and the carrier trapping. It is followed by a recombination process of trapped carriers at later delay time. (c) 2007 American Institute of Physics.
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Beta gallium oxide (beta-Ga2O3) single crystals were grown by the floating zone technique. The absorption spectra and the luminescence of the crystals were measured. The absorption spectra showed an intrinsic short cutoff edge around 260 nm with two shoulders at 270 and 300 nm. Not only the characteristic UV (395 nm), blue (471 nm) and green (559 nm) lights, but also the red (692 nm) light can be seen in the emission spectra. The deep UV light was attributed to the existing of quantum wells above the valence band and the red light was owed to the electron-hole recombination via the vicinity donors and acceptors. (c) 2006 Elsevier Ltd. All rights reserved.
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聚合酶链式反应(Polymerase Chain Reaction,PCR)技术从其发明以来,因为其操作的简单方便和高效率而在生物学研究的各个领域得到了广泛的应用,包括序列扩增、序列的人工突变、疾病诊断、法医学鉴定、基因的表达分析等等。从PCR技术发明以来,如何提高反应的特异性和反应的效率一直是人们所共同关心的题目,为此也发展了相当数量的各种方法,如热启动PCR、降落PCR、巢式PCR以及在反应体系中添加一些有益的附属物等。而适合不同目的的PCR技术也得到了充分的发展,如多重PCR、反转录PCR、定量PCR、原位PCR、PCR突变、毛细管PCR技术等等。并且,包括随机引物扩增多态、扩增片段长度多态性、简单重复序列多态性、单核苷酸多态性等这些在PCR技术基础上发展而来的各种分子标记技术极大地方便了遗传分析和遗传图谱的构建等工作。在PCR技术发明了20年后的今天,提高PCR的反应性能、发展适合新领域的PCR技术和新的分子标记技术仍然是研究者关心的题目和努力的方向。 PCR实验中已经观察到多种异常现象,除了常见的扩增失败(没有产物)、扩增产物特异性不强(有非特异产物出现)、引物多聚体产物扩增、扩增效率低等现象以外,还包括PCR介导的重组、跳跃、复制滑动等等。阐明这些异常现象的发生机理和过程,避免或缓解这些异常现象在扩增过程中对目的产物扩增的影响,以及促进和利用一些特殊的异常PCR扩增都是PCR技术研究所关心的话题。各种研究工作中经常需要扩增一些长片段的序列,但是在进行长片段PCR时经常会发现扩增目标序列的长度是有限的、扩增效率比较低、扩增产物检测中有很强的背景弥散等现象;同时长片段PCR需要一些特殊的反应体系组成和反应条件。如何更加有效地实现更长序列的PCR扩增也是人们所关心的话题之一。 常见的PCR产物重复扩增(以上一轮扩增产物为模板进行新的PCR扩增)扩增轮数少,通常仅进行一次重复扩增;同时,在重复扩增中常使用的策略是使用巢式引物。而连续PCR扩增实验(用相同的引物以产物为模板进行多轮次的连续重复PCR扩增)从未见于文献报道。我们第一次系统地进行了连续PCR扩增实验;同时,在实验过程中我们观察到了一种新的PCR扩增异常现象——用不同来源的模板(病毒、细菌质粒或真核生物来源的DNA序列)进行连续PCR扩增不同长度的靶序列,经过有限次数的重复扩增后,最终都会导致扩增失败;这种扩增失败都表现为在常规琼脂糖电泳检测时特异产物条带的消失和不能泳动出点样孔之复杂异常产物的出现;这种扩增产生的异常产物能够被稳定地重复扩增。用λ和细菌质粒序列为模板连续扩增不同长度靶序列的结果表明:连续PCR扩增失败的时期具有扩增靶序列长度的依赖性,越长的靶序列在连续PCR中扩增失败的时期越早。 对不同连续PCR扩增的扩增过程观察表明扩增产物经历了一个从高效特异性扩增到低效率特异性扩增,再到扩增产生复杂异常产物的过程。对复杂异常产物的甲酰胺辅助变性处理和变性胶电泳(尿素变性聚丙烯酰胺胶电泳和NaOH碱变性琼脂糖电泳)检测表明扩增产生的复杂产物主要由连续分布的小于靶序列长度的具有相当程度多样性的非全长链组成。连续PCR产生的复杂产物在内部具有局部的双链区域和大量的单链区域及外部单链分支,能够被单链特异的S1核酸酶消化,但是不能被双链特异的限制性内切酶消化。用DNase I或限制性内切酶处理连续扩增早期产生特异扩增产物形成不同长度序列组成的混合物,或者直接用不同扩增反应产生的不同长度的核酸序列组成混合物,混合物在经历变性-复性后都表现出类似连续PCR失败所产生的异常产物电泳行为。这些证据都表明PCR扩增过程中形成的非全长链成分是导致这种异常现象的关键因素,多个不同长度的非全长链复性形成“杂种分子”(具有较大且不一致的分子量和复杂的分支结构),最终表现为常规琼脂糖电泳异常的复杂产物。同时,异常产物组成非全长链成分和全长链成分是其能够实现稳定重复扩增的基础。 实验结果表明:对于特定长度的靶序列而言,导致复杂异常出现的根本原因是连续PCR扩增体系中所经历的总PCR热循环数目(每一轮PCR扩增所使用的循环数目多,成功连续扩增的轮数就少);而扩增体系中的引物浓度、DNA聚合酶用量的多少、扩增程序中时间参数等对此影响较小;巢式PCR和单引物-互补引物PCR的结果表明这些处理对于缓解或延迟异常产物的出现有一定的作用。人工处理(DNase I或限制性内切酶处理)完整模板双链形成的非全长链长产物,然后把非全长链长产物以不同比例同完整模板混合模拟连续扩增后期产物,这种人工混合模板表明连续PCR扩增中同源的非全长链成分对PCR扩增有严重的干扰作用,是导致复杂异常产物出现的直接原因。 已有的研究表明:PCR介导重组、长片段PCR难于操作有共同的产生基础——扩增过程中非全长链成分的产生和非全长链成分对后续扩增过程的干扰作用。这一点和导致连续PCR失败的原因是一致的。非全长链成分的出现是PCR扩增过程中不可避免的,其最初产生的可能来源有三个:模板的损伤(扩增前的模板损伤或扩增热循环过程中的损伤)、聚合酶的忠实性、以及聚合酶的进行性。根据聚合酶的特性而调整扩增程序中延伸时间的实验表明,聚合酶的进行性不是导致连续PCR扩增失败的最主要原因。这种非全长链成分产物从无到有且不依赖于体系中非全长链成分的过程我们称之为非全长链成分的初级合成;而已经存在的非全长链成分干扰后续合成形成非全长链成分的过程我们称之为非全长链成分的次级合成。非全长链成分的初级合成和次级合成共同导致了连续扩增的失败和异常产物的形成。 从已有的研究结果看,任何降低PCR扩增过程中非全长链成分产生的措施,特别是聚合酶忠实性的提高,都能缓解异常扩增产物的出现和利于长片段PCR操作。
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利用RNA减法杂交、差异筛选和5’-RACE等方法从水稻分离到了一花药绒毡层特异表达的基因RA39。Southern 杂交表明,RA39在水稻基因组中是以单拷贝的形式存在的。RT-PCR 结果初步表明,RA39是一水稻花药特异表达的基因。RNA原位杂交进一步表明,RA39主要在水稻花药的绒毡层中表达,而且在小孢子母细胞减数分裂期和四分体时期表达量最高。RA39 cDNA全长1013bp,编码298个氨基酸残基。 RA39 cDNA与数据库中的已知序列没有明显的相似性,由其推测的多肽与核糖体失活蛋白(ribosome-inactivating protein, RIP)的序列相似在19-34%之间。多重序列排列分析结果表明构成RIPs活性位点的5个关键氨基酸残基在RA39中是保守的,在蓖麻毒蛋白中分别为Tyr80、 Tyr123、 Glu177、 Arg180 and Trp211 。利用原核表达系统,通过蛋白质分离和纯化获得了在SDS电泳图谱上为单一条带的纯的RA39蛋白,用兔rRNA作底物进行的酶活性分析证明该蛋白有N-糖基化作用,是一种类型I的核糖体失活蛋白。反义转基因植株的花粉用TTC进行活性染色结果显示其活性明显减弱,成熟的T0代反义转基因植株的结实率明显降低,只有对照的20-60%。这说明,RA39蛋白可能和小孢子母细胞的发育相关。 酵母DMC1是减数分裂过程中同源染色体配对和重组修复所必需的减数分裂特异基因。根据酵母Dmc1和拟南芥AtDmc1的保守区设计简并性引物,通过RT-PCR和RACE等方法,从水稻中分离出了酵母DMC1的同源基因OsDMC1。RT-PCR分析表明,OsDMC1在花中表达量最高,在根中表达量较低,在叶片和幼芽几乎不表达。水稻基因组中有两个拷贝的OsDMC1。OsDmc1蛋白与酵母Dmc1和拟南芥AtDmc1氨基酸一致性分别为53%和81%。 酵母Spo11在减数分裂过程中具有催化DNA双链断裂从而起始同源重组的功能。以酵母Spo11氨基酸序列为探针和现有的数据库通过数据分析,结合RACE技术,克隆了水稻SPO11同源基因OsSPO11-1, OsSPO11-1是一个单拷贝基因,有3个外显子和2个内含子,在转录过程中通过内含子的可变剪切产生4个不同的转录本(OsSPO11-1A、OsSPO11-1B、OsSPO11-1C和OsSPO11-1),其中,OsSPO11-1A是一个未剪切的转录本,OsSPO11-1B包含内含子2,OsSPO11-1C包含内含子1,OsSPO11-1D是一个完全剪切的转录本。这些转录本编码的蛋白有一致的246氨基酸残基的C-端,包含了Spo11/TopVIA家族蛋白共有的5个功能基元,是该家族的新成员。OsSPO11-1A和 OsSPO11-1C在花中优势积累,OsSPO11-1B是花特异的,而OsSPO11-1D在营养器官中优势积累。在花中该基因主要在减数分裂的花粉母细胞和胚曩中表达,在减数分裂期的绒毡层细胞和不同花器官的微管束细胞中也表达。这些结果说明内含子涉及到了OsSPO11-1表达的器官特异性调节,该基因除了参与减数分裂的调节外,在体细胞的发育中可能起重要作用。
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本论文以显花植物水稻和拟南芥为对象,研究植物器官形成激素调控的分子机理。发现拟南芥干细胞决定基因WUS和ABA信号关键调节因子ABI3间存在相互调节关系,它们对质体和根毛发育等具有调控作用;运用细胞学手段对OsAGAP和OsRMC调控根发育的机理进行了研究。这些结果为了解ABA、生长素和JA等激素对分生组织或根等器官的形成的调控机理提供了新资料。 拟南芥WUS基因是一个重要的干细胞决定基因。在茎尖分生组织和花分生组织的动态平衡调节中各存在一个反馈调节环:WUS促进CLV3的表达,而CLV3 反馈抑制WUS表达,它们共同决定干细胞的数目;在WUS+LFY 和AG之间也存在一个类似的反馈环,负责花器官的正常启动和终止。本工作发现在外源ABA 存在下,拟南芥WUS功能获得突变体sef (stem ectopic flowers)子叶黄化过程受到抑制,即sef突变体对ABA 的敏感性降低,而且在sef突变体中ABI3转录水平下调,说明WUS 抑制ABI3的表达。另一方面,在abi3突变体中WUS转录水平下降,启动子分析发现WUS是ABI3所在的B3结构域家族基因的靶基因,酵母单杂交实验表明B3家族蛋白FUS3可以与WUS调控区结合;外源ABA 处理pWUS::GUS植株发现ABA可使WUS异位表达,暗示受ABA信号诱导的B3类转录因子可与WUS调控区结合,从而促进WUS的表达。这些结果支持ABI3/WUS间的反馈调节机理,该调节环可能参与调控拟南芥质体和根毛发育等过程。 双子叶和单子叶植物的发育和器官形成高度依赖生长素极性运输(PAT), 生长素输入和输出载体的准确定位对于极性运输的正常进行是必要的。在双子叶模式植物拟南芥中,生长素输出载体PIN1的转运和定位受小G蛋白ARF鸟苷酸转换因子GNOM介导。本实验室克隆到一个水稻ARF GAPase激活蛋白OsAGAP, 其超表达引起PAT改变且干扰主根和侧根的发生及发育。前期生理实验显示超表达植株侧根的表型可被膜渗透性生长素NAA恢复,但不能被载体依赖型生长素IAA和2, 4-D恢复。为了解释OsAGAP过表达引起根系发育受到抑制的表型,本工作主要从细胞学角度继续深入分析OsAGAP介导生长素运输的机理。实验发现,OsAGAP超表达植株中AUX1在细胞中分布改变;生长素输出载体PIN1和PIN2的定位不受影响;该基因的超表达使囊泡聚集,形成类似囊泡运输抑制剂BFA处理后的结构;OsAGAP与细胞转运系统中的高尔基体存在部分共定位。以上结果表明OsAGAP调节小G蛋白Arf的活性,参与调控生长素极性运输过程,进而调控根系发育。通过对JA诱导的OsRMC蛋白的膜定位分析及转基因植株根中JA合成水平的测定,为研究此蛋白参与JA信号、调控根系发育提供了直接证据。 此外,论文还对拟南芥STAR2基因的功能进行了一定的初探。
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Antimicrobial peptides secreted by the skin of many amphibians play an important role in innate immunity. From two skin cDNA libraries of two individuals of the Chinese red belly toad (Bombina maxima), we identified 56 different antimicrobial peptide cDNA sequences, each of which encodes a precursor peptide that can give rise to two kinds of antimicrobial peptides, maximin and maximin H. Among these cDNA, we found that the mean number of nucleotide substitution per non-synonymous site in both the maximin and maximin H domains significantly exceed the mean number of nucleotide substitution per synonymous site, whereas the same pattern was not observed in other structural regions, such as the signal and propiece peptide regions, suggesting that these antimicrobial peptide genes have been experiencing rapid diversification driven by Darwinian selection. We cloned and sequenced seven genes amplified from skin or liver genomic DNA. These genes have three exons and share the same gene structure, in which both maximin and maximin H are encoded by the third exon. This suggests that alternative splicing and somatic recombination are less likely to play a role in creating the diversity of maximins and maximin Hs. The gene trees based on different domain regions revealed that domain shuffling or gene conversion among these genes might have happened frequently.
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Due to its specific characteristics, such as maternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it harbors. Rare mutation (excluding parallel mutation) occurring at multiple times in different haplogroups could thus be a potential reading error according to the mtDNA phylogeny. This experience has been widely used in double-checking the credibility of the rare mutations in human mtDNA sequences. However, no test has been performed so far for the feasibility of applying this strategy to the rare insertion/deletion (indel) events in mtDNA sequences. In this study, we attempted to relate the rare indels in mtDNAs to their haplogroup status in a total of 2352 individuals from 50 populations in China. Our results show that the insertion of A at position 16259 is restricted to a subclade of haplogroup C and can be verified. The other indel polymorphisms, which occur in the repeat of the deleted or inserted nucleotide(s), may not be distinguished from phantom mutations from a phylogenetic point of view. Independently and multiply sequencing the fragment with the indel is the best and the most reliable way for confirmation.
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To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.
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The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyr
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Mutations in the long-range limb-specific cis-regulator (ZRS) could cause ectopic shh gene expression and are responsible for preaxial polydactyly (PPD). In this study, we analyzed a large Chinese isolated autosomal dominant PPD pedigree. By fine mapping
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Background: A single case of paternal co-transmission ofmitochondrial DNA (mtDNA) in humans has been reported so far. Objective: To find potential instances of non-maternal inheritance of mtDNA. Methods: Published medical case studies (of single patients) were searched for irregular mtDNA patterns by comparing the given haplotype information for different clones or tissues with the worldwide mtDNA database as known to date-a method that has proved robust and reliable for the detection of flawed mtDNA sequence data. Results: More than 20 studies were found reporting clear cut instances with mtDNAs of different ancestries in single individuals. As examples, cases are reviewed from recent published reports which, at face value, may be taken as evidence for paternal inheritance of mtDNA or recombination. Conclusions: Multiple types (or recombinant types) of quite dissimilar mitochondrial DNA from different parts of the known mtDNA phylogeny are often reported in single individuals. From re-analyses and corrigenda of forensic mtDNA data, it is apparent that the phenomenon of mixed or mosaic mtDNA can be ascribed solely to contamination and sample mix up.
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In plants and less-advanced animal species, such as C.elegans, introduction of exogenous double-stranded RNA (dsRNA) into cells would trigger degradation of the mRNA with homologous sequence and interfere with the endogenous gene expression. It might represent an ancient anti-virus response which could prevent the mutation in the genome that was caused by virus infection or mobile DNA elements insertion. This phenomenon was named RNA interference, or RNAi. In this study, RNAi was used to investigate the function of basonuclin gene during oogenesis. Microinjection of dsRNA directed towards basonuclin into mouse germinal-vesicle-intact (GV) oocytes brought down the abundance of the cognate mRNA effectively in a time- and concentration-dependent manner. This reduction effect was sequence-specific and showed no negative effect on other non-homologous gene expression in oocytes, which indicated that dsRNA can recognize and cause the degradation of the transcriptional products of endogenous basonuclin gene in a sequence-specific manner. Immunofluorescence results showed that RNAi could reduce the concentration of basonuclin protein to some extent, but the effect was less efficient than the dsRNA targeting towards tPA and cMos which was also expressed in oocytes. This result might be due to the long half life of basonuclin protein in oocytes and the short reaction time which was posed by the limited life span of GV oocytes cultured in vitro. In summary, dsRNA could inhibit the expression of the cognate gene in oocytes at both mRNA and protein levels. The effect was similar to Knock-out technique which was based on homologous recombination. Furthermore, hairpin-style dsRNA targeting basonuclin gene could be produced by transcription from a recombinant plasmid and worked efficiently to deplete the cognate mRNA in oocytes. This finding offered a new way to study the function of basonuclin in the early stage of oogenesis by infection of primordial oocytes with the plasmid expressing hairpin-style basonuclin dsRNA.
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There is increasing evidence that many of the mitochondrial DNA (mtDNA) databases published in the fields of forensic science and molecular anthropology are flawed. An a posteriori phylogenetic analysis of the sequences could help to eliminate most of the errors and thus greatly improve data quality. However, previously published caveats and recommendations along these lines were not yet picked up by all researchers. Here we call for stringent quality control of mtDNA data by haplogroup-directed database comparisons. We take some problematic databases of East Asian mtDNAs, published in the Journal of Forensic Sciences and Forensic Science International, as examples to demonstrate the process of pinpointing obvious errors. Our results show that data sets are not only notoriously plagued by base shifts and artificial recombination but also by lab-specific phantom mutations, especially in the second hypervariable region (HVR-II). (C) 2003 Elsevier Ireland Ltd. All rights reserved.
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Gene mapping of a mouse coat mutation has been investigated. First, 100 10-bp random primers were used to amplify DNA, but the mutation could not be located by this method because there were no correlation between the amplified products and coat phenotypes. Second, by using Idh1, Car2, Mup1, Pgb1, Hbb, Es10, Es1, Mod1, Gdc1, Ce2, Es3 as genetic markers, linkage test crosses (two-point test) consisting of intercrossing uncovered BALB/c mice (homozygotes) to CBA/N and C57BL/6 mice with normal hair and backcrossing the heterozygotes of the F1 to the uncovered BALB/c mice were made. It was soon evident that the mutation was linked to Es3 on chromosome 11. Furthermore, three-point test was made by using Es3 and D11Mit8 (a microsatellite DNA) as genetic markers. The result showed that the mutation was linked to Es3 with the percentage recombination of (7.89 +/- 2.19)%, and linked to D11Mit8 with the percentage recombination of (26.38 +/- 3.57)%. The percentage recombination between Es3 and D11Mit8 was (32.90 +/- 3.81)%. The mutation was named Uncovered, with the symbol Uncv. According to the recombinations, the loci order was D11Mit8-26.30 +/- 3.57- Uncv-7.89 +/- 2.19-Es3. From the location on the chromosome, it was concluded that the mutation was a new mutation which affected the skin and hair structure of mouse. The Uncv has entered MGD (Mouse Genome Database).
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Objectives: To investigate the molecular epidemiology of HIV in China's Yunnan Province, where the initial HIV-1 outbreak among injecting drug users (IDU) occurred in 1989, and to analyse the genesis and interrelationship of the epidemic with that in surrounding areas. Design: A molecular epidemiological investigation was conducted among IDU in three prefectures in Yunnan Province, including Wenshan (east), Honghe (southeast) and Dehong (west). Methods: Thirty-nine specimens were collected from consenting IDU in 2000-2001. The nucleotide sequences of 2.6 kb gag-RT and 340 base pair (bp) env (C2/V3) regions were determined. Phylogenetic tree and recombination breakpoint analyses were performed. Results: The circulating recombinant form (CRF), CRF08_BC, predominated in east Yunnan near Guangxi Province (89% in Wenshan and 81% in Honghe), whereas it was not detected in Dehong(0/14) in the west. In contrast, 71% (10/14) of the Dehong isolates were unique recombinant forms (URF), mostly between subtypes B' (Thailand variant of subtype B) and C, with distinct profiles of recombination breakpoints. The subtype B' accounts for the remaining 29% (4/14) of Dehong isolates. Interestingly, two Honghe isolates (2/16) shared some of the precise B'/C recombination breakpoints with CRF07_BC. Conclusion: New recombinant strains are arising continually in west Yunnan near the Myanmar border. Some appeared to be secondary recombinants derived from CRF07_BC that had further recombined with other strains. The uneven distribution of subtypes, CRF and URF, suggests the presence of independent transmission networks and clusters among IDU in Yunnan. (C) 2002 Lippincott Williams Wilkins.