Magnification of the rDNA cluster in Kluyveromyces lactis

Summary By employing pulsed field gel electrophoresis we find that slow growing strains of Kluyveromyces lactis have only 43%–55% of the wild-type level of ribosomal DNA (rDNA) repeats. When subjected to prolonged vegetative growth these strains can increase both the number of rDNA repeats and their growth rate.     

A Two-Stage Model for the Control of rDNA Magnification

Males of the genotype bb/Ybb- have been shown to produce both magnified (bbm+) and, less frequently, reduced (bbrl) X chromosomes. An analysis of the progeny of single magnifying bb/Ybb- males reveals that bbm+ revertants may be recovered either as rare single events or, more frequently, in large clusters. To analyze the role of the bb phenotype in the induction of rDNA magnification we have constructed a series of bb and bb+ derivatives of Ybb-. Males carrying an X chromosomal bb allele and one of these derivatives (bb/bbYbb- or bb/bb+Ybb-) produce small numbers (one to two) of bbm+ progeny at a frequency similar to that observed for bb/Ybb- males but do not produce large clusters of bbm+ revertants. In addition, bb/bb+Ybb- males produce essentially equal numbers of magnified (bbm+) and reduced (bbrl) X chromosomes. These data, together with a consideration of the growth properties of the male germline in Drosophila, suggest that magnification/reduction may occur at two different times during development. Those events that give rise to large clusters, and, thus, necessarily arise early in germ cell development, appear to be dependent on the bb phenotype. However, those events that give rise to single bbm+ chromosomes arise late in spermatogenesis, probably at meiosis, and are independent of the bb phenotype.     

Ring Chromosomes and rDNA Magnification in Drosophila

Tartof showed that ribosomal gene magnification in Drosophila was inhibited in a ring X chromosome. The present studies extend this observation by showing that ring X chromosomes are lost meiotically in male Drosophila undergoing ribosomal gene magnification as evidenced by the recovery of a lower number of ring-bearing progeny under magnifying conditions compared with nonmagnifying conditions. Associated with ring chromosome loss is a highly significant increase in the number of double-sized dicentric ring chromosomes in meiotic cells from magnifying males. These observations explain the failure of ring X chromosomes to magnify and imply that magnification in rod chromosomes occurs via a mechanism of unequal sister chromatid exchange. Our results support the hypothesis that the primary event of magnification is a sister chromatid exchange in the rDNA, that the frequency of sister strand exchanges is increased in magnifying flies, that a significant number of exchanges in magnifying flies occurs meiotically and that some of the exchanges are nonreciprocal. We have also found that autosomal mutations can affect both the frequency of abnormal ring structures and the ability of ring X chromosomes to magnify.     

Copy Number of the Transposon,Pokey, in rDNA Is Positively Correlated with rDNA Copy Number in Daphnia obtusa

Pokey is a class II DNA transposon that inserts into 28S ribosomal RNA (rRNA) genes and other genomic regions of species in the subgenus, Daphnia. Two divergent lineages, PokeyA and PokeyB have been identified. Recombination between misaligned rRNA genes changes their number and the number of Pokey elements. We used quantitative PCR (qPCR) to estimate rRNA gene and Pokey number in isolates from natural populations of Daphnia obtusa, and in clonally-propagated mutation accumulation lines (MAL) initiated from a single D. obtusa female. The change in direction and magnitude of Pokey and rRNA gene number did not show a consistent pattern across ∼87 generations in the MAL; however, Pokey and rRNA gene number changed in concert. PokeyA and 28S gene number were positively correlated in the isolates from both natural populations and the MAL. PokeyB number was much lower than PokeyA in both MAL and natural population isolates, and showed no correlation with 28S gene number. Preliminary analysis did not detect PokeyB outside rDNA in any isolates and detected only 0 to 4 copies of PokeyA outside rDNA indicating that Pokey may be primarily an rDNA element in D. obtusa. The recombination rate in this species is high and the average size of the rDNA locus is about twice as large as that in other Daphnia species such as D. pulicaria and D. pulex, which may have facilitated expansion of PokeyA to much higher numbers in D. obtusa rDNA than these other species.     

Ribosomal Gene Magnification in Drosophila: A Chromosomal Change

The sex-linked mutant "bobbed" can undergo a rapid phenotypic reversion during a prescribed series of outcrosses. The experiments reported here distinguish between two general genetic models. The first is that the phenotypic change results from the changing genetic background brought about by the outcrosses. The second is that the phenotypic change results from an alteration of the X chromosome in the germ line. The data support the second model. It is shown that both the bobbed and reverted phenotypes segregate from the same female. In addition, the reverted phenotype maps in or near the proximal heterochromatin of the X chromosome, which is the standard map position of both bobbed and the nucleolus organizer.     

巴氏钝绥螨rDNA的ITS基因片段序列分析

采用酚-氯仿抽提法提取了采自江西赣南的巴氏钝绥螨Amblyseiusbarkeri Hughes,1948基因组DNA。以相应引物对巴氏钝绥螨核糖体ITS基因进行PCR扩增,直接测序,得到了652bp的碱基片段（国际基因库索引号FJ392365）,其碱基序列A、C、G、T含量分别为193bp（29．60％）、114bp（17．48％）、144bp（22．09％）、201bp（30．83％）,并对其与其他植绥螨5．8SrDNA及两侧ITS序列进行了分析。     

基于PACS的影像学检查流程优化研究

为了推行惠民便民措施,优化就医流程、降低候诊时间,切实解决“看病难”问题,提出了优化整合PACS（医学影像存储和传输系统）,整合以放射线科、磁共振室、CT室为主要科室,以信息流代替患者流为主要改进方式,以预约登记、检查诊断、数字传输、信息存储为主要功能的一体化综合诊断管理平台。基于PACS的影像学检查流程优化对于提升临床诊断水平、降低患者候诊时间、降低科室运营成本、缓解“看病难、看病贵”有着重大意义。     

Evidence for an excess of rDNA in the testis of Drosophila melanogaster during rDNA magnification.

Summary Hybridization of rRNA with DNA extracted from different tissues of different genotypes have been performed. The results show that: 1) in DNA extracted from the testis of premagnified males there exists an excess of rDNA, which is consistent with the model proposed by Ritossa (1972) and by us (1973) to explain the phenomenon of magnification. 2) in DNA extracted from diploid tissues of different genotypes the percent of rDNA is directly proportional to the number of ribosomal genes. 3) in polytene cells the percent of rDNA for all genotypes so far studied is less than that in diploid cells and is not significantly dependant on the genotype. This last result is consistent with those of Spear and Gall (1973).     

Copy Number Variants in the Kallikrein Gene Cluster

The kallikrein gene family (KLK1-KLK15) is the largest contiguous group of protease genes within the human genome and is associated with both risk and outcome of cancer and other diseases. We searched for copy number variants in all KLK genes using quantitative PCR analysis and analysis of inheritance patterns of single nucleotide polymorphisms. Two deletions were identified: one 2235-bp deletion in KLK9 present in 1.2% of alleles, and one 3394-bp deletion in KLK15 present in 4.0% of alleles. Each deletion eliminated one complete exon and created out-of-frame coding that eliminated the catalytic triad of the resulting truncated gene product, which therefore likely is a non-functional protein. Deletion breakpoints identified by DNA sequencing located the KLK9 deletion breakpoint to a long interspersed element (LINE) repeated sequence, while the deletion in KLK15 is located in a single copy sequence. To search for an association between each deletion and risk of prostate cancer (PC), we analyzed a cohort of 667 biopsied men (266 PC cases and 401 men with no evidence of PC at biopsy) using short deletion-specific PCR assays. There was no association between evidence of PC in this cohort and the presence of either gene deletion. Haplotyping revealed a single origin of each deletion, with most recent common ancestor estimates of 3000-8000 and 6000-14 000 years for the deletions in KLK9 and KLK15, respectively. The presence of the deletions on the same haplotypes in 1000 Genomes data of both European and African populations indicate an early origin of both deletions. The old age in combination with homozygous presence of loss-of-function variants suggests that some kallikrein-related peptidases have non-essential functions.     

Identification of Mytilus spp. and Pecten maximus in Irish Waters by Standard PCR of the 18S rDNA Gene and Multiplex PCR of the 16S rDNA Gene

Two molecular protocols for the identification of mussel and scallop have been developed using specific primers targeting the mitochondrial 16S ribosomal DNA gene and the nuclear 18S ribosomal DNA gene. Primers for the mitochondrial 16S ribosomal DNA gene in multiplex polymerase chain reaction (PCR) protocols yielded diagnostic DNA fragments for the mussels Mytilus edulis, Mytilus galloprovincialis, and the hybrid Mytilus edulis/galloprovincialis (335 bp), the king scallop Pecten maximus (382 bp) and the black scallop Mimachlamys varia (398 bp). DNA from the queen scallop Aequipecten opercularis showed no consistent PCR amplification of the 16S rDNA gene. Primers for the nuclear 18S rDNA gene in standard PCR protocols yielded similar-sized, diagnostic DNA fragments (approx. 190 bp) for the mussels Mytilus edulis, Mytilus galloprovincialis, and the hybrid Mytilus edulis/galloprovincialis, the king scallop Pecten maximus, the black scallop Mimachlamys varia, and the queen scallop Aequipecten opercularis. Both protocols have been tested with Mytilus spp., P. maximus, and 6 other bivalve species from a wide range of locations in Irish and European waters. Cross reaction of the specific primers with DNA template from any of the 6 other bivalve species was not observed. Rapid DNA extraction using FTA Card technology and the16S rDNA primers allowed for the detection of at least 10 mussel larvae in a subsample of natural plankton.     

The Question of the Total Gene Number in DROSOPHILA MELANOGASTER

A statistical analysis has been carried out on the distribution and allelism of nearly 500 sex-linked, X-ray-induced, cytologically normal and rearranged lethal mutations in Drosophila melanogaster that were obtained by G. Lefevre. The mutations were induced in four different regions of the X chromosome: (1) 1A1-3E8, (2) 6D1-8A5, (3) 9E1-11A7 and (4) 19A1-20F4, which together comprise more than one-third of the entire chromosome.--The analysis shows that the number of alleles found at different loci does not fit a Poisson distribution, even when the proper procedures are taken to accommodate the truncated nature of the data. However, the allele distribution fits a truncated negative binomial distribution quite well, with cytologically normal mutations fitting better than rearrangement mutations. This indicates that genes are not equimutable, as required for the data to fit a Poisson distribution.--Using the negative binomial parameters to estimate the number of genes that did not produce a detectable lethal mutation in our experiment (n0) gave a larger number than that derived from the use of the Poisson parameter. Unfortunately, we cannot estimate the total numbers of nonvital loci, loci with undetectable phenotypes and loci having extremely low mutabilities. In any event, our estimate of the total vital gene number was far short of the total number of bands in the analyzed regions; yet, in several short intervals, we have found more vital genes than bands; in other intervals, fewer. We conclude that the one-band, one-gene hypothesis, in its literal sense, is not true; furthermore, it is difficult to support, even approximately.--The question of the total gene number in Drosophila will, not doubt, eventually be solved by molecular analyses, not by statistical analysis of mutation data or saturation studies.     

45S rDNA基因的不稳定性及其与转录的相关性

45S rDNA基因由串联重复序列构成,是遗传不稳定性的热点区域,易于发生DNA断裂和重组。以Hela和CHO细胞系为研究对象,运用荧光原位杂交技术检测有丝分裂不同时期的45S rDNA基因的不稳定性表型。结果表明,位点特异性的染色体浓缩失败是其在中期染色体上不稳定性的主要表型。具有这种表型的染色体在后期可能会出现落后或粘连现象,甚至有可能引发断裂,形成卫星核。同时,免疫荧光双染色技术检测表明DNA双链断裂的标记蛋白(γH2AX)和RNA聚合酶I的上游结合因子(UBF)在有丝分裂的不同时期都存在共定位现象。该结果为探讨45S rDNA基因的不稳定性与转录的关系提供了直观的细胞学证据。     

Evolution of the F-Box Gene Family in Euarchontoglires: Gene Number Variation and Selection Patterns

F-box proteins are substrate adaptors used by the SKP1–CUL1–F-box protein (SCF) complex, a type of E3 ubiquitin ligase complex in the ubiquitin proteasome system (UPS). SCF-mediated ubiquitylation regulates proteolysis of hundreds of cellular proteins involved in key signaling and disease systems. However, our knowledge of the evolution of the F-box gene family in Euarchontoglires is limited. In the present study, 559 F-box genes and nine related pseudogenes were identified in eight genomes. Lineage-specific gene gain and loss events occurred during the evolution of Euarchontoglires, resulting in varying F-box gene numbers ranging from 66 to 81 among the eight species. Both tandem duplication and retrotransposition were found to have contributed to the increase of F-box gene number, whereas mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes, resulting in a balance of expansion and contraction in the F-box gene family. Thus, the Euarchontoglire F-box gene family evolved under a birth-and-death model. Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins, and adaptive changes played a role in evolution of the Euarchontoglire F-box gene family. In addition, single nucleotide polymorphism (SNP) distributions were found to be highly non-random among different regions of F-box genes in 1092 human individuals, with domain regions having a significantly lower number of non-synonymous SNPs.     

Rapid Evolution of the Mammalian HILS1 Gene and the Nuclear Condensation Process during Mammalian Spermiogenesis

Many genes associated with reproduction show rapid evolution across diverse animal groups,a result commonly due to adaptive evolution driven by positive selection(Swanson and Vacquier,2002).Different theories have been proposed to explain the elevated rates of evolution(Swanson and Vacquier,2002),including sperm competition,where sperm compete to fertilize eggs leading to the proteins in the sper- matozoa adaptively evolving to increase their ability to fertilize eggs;sexual conflict,where the egg experiences a loss     

基因组拷贝数变异研究进展

基因组结构变异分为两个层次:显微水平(microscopic)和亚显微水平(submicroscopic)。显微水平的基因组结构变异主要是指显微镜下可见的染色体畸变,包括整倍体或非整倍体、缺失、插入、倒位、易位、脆性位点等结构变异。亚显微水平的基因组结构变异是指DNA片段长度在1Kb-3Mb的基因组结构变异,包括缺失、插入、重复、重排、倒位、DNA拷贝数目变化(copy numbervariation,CNV),这些统称为CNV或者CNP(copy number polymorphisms,CNP)。对CNV的研究能够帮助研究者建立遗传检测假说,进而发现疾病易感基因,同时加深对表型变异的理解,为今后研究人类生物功能、进化、疾病奠定基础。本文主要从CNV的研究历史、分子机制、研究方法、研究意义等四个方面进行综述.。