High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer

Several DNA sequences similar to the mariner element were isolated and characterized in the platyhelminthe Dugesia (Girardia) tigrina. They were 1,288 bp long, flanked by two 32 bp-inverted repeats, and contained a single 339 amino acid open-reading frame (ORF) encoding the transposase. The number of copies of this element is approximately 8,000 per haploid genome, constituting a member of the middle- repetitive DNA of Dugesia tigrina. Sequence analysis of several elements showed a high percentage of conservation between the different copies. Most of them presented an intact ORF and the standard signals of actively expressed genes, which suggests that some of them are or have recently been functional transposons. The high degree of similarity shared with other mariner elements from some arthropods, together with the fact that this element is undetectable in other planarian species, strongly suggests a case of horizontal transfer between these two distant phyla.      

The Dugesia ryukyuensis database as a molecular resource for studying switching of the reproductive system

The planarian Dugesia ryukyuensis reproduces both asexually and sexually, and can switch from one mode of reproduction to the other. We recently developed a method for experimentally switching reproduction of the planarian from the asexual to the sexual mode. We constructed a cDNA library from sexualized D. ryukyuensis and sequenced and analyzed 8,988 expressed sequence tags (ESTs). The ESTs were analyzed and grouped into 3,077 non-redundant sequences, leaving 1,929 singletons that formed the basis of unigene sets. Fifty-six percent of the cDNAs analyzed shared similarity (E-value<1E -20) with sequences deposited in NCBI. Highly redundant sequences encoded granulin and actin, which are expressed in the whole body, and other redundant sequences encoded a Vasa-like protein, which is known to be a component of germ-line cells and is expressed in the ovary, and Y-protein, which is expressed in the testis. The sexualized planarian expressed sequence tag database (http://planaria.bio.keio.ac.jp/planaria/) is an open-access, online resource providing access to sequence, classification, clustering, and annotation data. This database should constitute a powerful tool for analyzing sexualization in planarians.     

1株红海榄根际纤维素降解真菌的分离鉴定及其酶学性质

利用刚果红纤维素培养基,从海南三亚红海榄植物根际土壤中筛选得到1株纤维素降解真菌,将其命名为Z-2-4.形态学初步鉴定结果为曲霉属(Aspergillus),对其ITS、β-微管蛋白(β-tubulin)、钙调节蛋白(calmodulin)基因序列进行了扩增并测序.结果表明:该菌的ITS序列与其亲缘关系最近的Aspergillus insulicola( EF661430.1)只有94％的相似性,β-微管蛋白序列与Aspergillus insulicola( FR775320.1)的相似性为89％,钙调节蛋白序列与Aspergillus insulicola( EF661396.1)的相似性为93％,推测该菌为Aspergillus属的1个新种.对该菌株进行了酶学性质的初步研究,结果显示该菌株所产纤维素酶的最佳反应温度为40℃,最佳反应pH值为6.0,产纤维素酶活力最高出现在发酵4天时,达到2.57 U/mL.     

Immunohistochemical detection of opsins in turbellarians

Using the antiserum against the C-terminus of opsin of Dugesia japonica, immunohistochemistry revealed that opsins were actually localized in the photoreceptive organs of several turbellarians. The antiserum produced positive reactions in eyes of the Polycladida Notoplana koreana as well as those of the Tricladida Dugesia dorotocephala, Bdellocephala brunnea, Phagocata kawakatsui, Phagocata vivida and Polycelis auriclata, but not to those of Convoluta naikaiensis, Stenostomum sp. and Macrostomum tuba. This suggests that these opsin proteins of triclad and polyclad species have functional similarity in the C-terminus. This revised version was published online in July 2006 with corrections to the Cover Date.     

Microbial diversity in ikaite tufa columns: an alkaline,cold ecological niche in Greenland

Ikaite tufa columns from the Ikka Fjord in south-western Greenland constitute a natural, stable environment at low temperature and with a pH ranging from neutral at the exterior to very alkaline (pH 10.4) at the interior of the column. Phylogenetic analysis of culturable organisms revealed ten different isolates representing three of the major bacterial divisions. Nine of the isolates showed 94-99% similarity to known sequences, whereas one isolate displayed a low degree of similarity (less than 90%) to a Cyclobacterium species. Seven of the isolates were shown to be cold active alkaliphiles, whereas three isolates showed optimal growth at neutral pH. Phylogenetic analysis of DNA isolated directly from the ikaite material demonstrated the presence of a microbial flora more diverse than the culturable isolates. Whereas approximately half of the phylotypes showed 90-99% similarity to known meso- or thermophilic alkaliphiles, the rest of the sequences displayed less than 90% similarity when compared to known 16S rRNA gene sequences in databases. Thus, in the present paper, we demonstrate that ikaite columns that host a specialized macroscopic flora and fauna also contain a unique, cold active, alkaliphilic microflora.     

Repeated DNA elements in planarians of the Dugesia gonocephala group (Platyhelminthes,Tricladida)

The results of the isolation of repetitive DNA elements in the genome of Dugesia etrusca, a species of the Dugesia gonocephala group, are reported. These sequences, about 1.4 kb long, represent only a part of longer interspersed genomic units (De1 family) and appear to be limited to the genome of some planarians of this group, as indicated by a Southern blot analysis performed in different species and populations. The genomic relationships among different species and populations of the D. gonocephala group are discussed in relation to the results obtained in the present work. This revised version was published online in July 2006 with corrections to the Cover Date.     

云南省日本三角涡虫不同地理种群mtDNA COⅠ基因序列分析及其系统发育

对采自中国云南省的日本三角涡虫(Dugesia japonica)13个地理种群的细胞色素C氧化酶I亚基基因(CO I)的部分片段进行PCR扩增、克隆和测序,以采自河南省的日本三角涡虫Luoyang种群为外群,用Clustal X 1.80、MEGA 4.0、PAUP*4.0、MrBayes 3.1.1等程序对其进行序...     

东北虎粪细菌区系的16S rRNA基因序列分析

为研究东北虎粪微生物区系建立了东北虎粪细菌的16SrDNA文库。通过EcoRⅠ和HindⅢ分别对阳性克隆进行酶切分析,从东北虎的16SrDNA文库中分别获得了15个具有酶切差异的克隆。BLAST分析结果显示,在15个克隆中,10个克隆与梭菌属成员有97%以上的同源性,其中有6个序列与诺维梭菌A型(Clostridiumnovyitype A)有99%的同源性,为诺维梭菌A型;4个序列与猪粪细菌RT-18B(Swine manure bacteriumRT-18B)有97%的同源性,为消化链球菌属(Peptostreptococcus)成员。其它序列与GenBank中登录的序列同源性低于97%,为5种未培养细菌,其中4种16SrRNA基因序列分别与Clostridiumpascui、破伤风梭菌E88(ClostridiumtetaniE88)、梭菌(Clostridiumsp.)14505及产气荚膜梭菌(Clostridiumperfringens)有94%~95%的相似性。第5种与肉杆菌(Carnobacteriumsp.)R-7279株有94%的同源性。     

The preference for movement direction in a T-maze in planarians

Characteristics of spatial orientation in T-maze were studied in 1768 Planaria of following types: Dugesia tigrina (sexless and sexual race), Dugesia lugubris, Ijmia tenuis, Bdellacephala punctata. It was shown that from one third to one half of individuals were characterized by asymmetry of movement direction preference. The preference of right turning was typical for Dugesia tigrina; Dugesia lugubris, Ijmia tenuis, Bdellacephala punctata preferred left turning. The asymmetry described is considered as a primitive form of species functional asymmetry.     

A small scale expression screen identifies tissue specific markers in the Dugesia japonica strain Pek-1

Freshwater planaria has tremendous capacity to reform the missing part of the body and therefore is considered as one of the most important model organism for regeneration study.At present,Schmidtea mediterranea and Dugesia japonica are the two major species utilized for laboratory manipulations.Dugesia japonica flatworms are widely distributed in the Far East including Cherry Valley region in the north-west area of Beijing,China.We reported here the establishment of an asexual Dugesia japonica strain Pek-1,as a suitable system for regeneration study.Using morphological,karyotypical as well as phyiogenetic analyses,we confirmed that these flatworms indeed belonged to Dugesia japonica.We went on to show that the commonly used in situ probes and immunohistochemistry reagents and protocols were applicable to the Pek-1 strain.Using this strain,we carried out small scale analysis on EST,RNAi and gene expression.We identified 193 unique EST sequences and 65 of them had not been reported in planarian.By RNAi analysis,we showed that 48 genes,when down-regulated individually,had no effect on regeneration.Furthermore,we identified 3 groups of tissue specific expressing genes that were useful for cell lineage analysis.We concluded that the Dugesia japonica Pek-1 swain could be another suitable animal model to regeneration research.     

Study of the heterogeneity of 16s rRNA gene and groESL operone in the dna samples of Anaplasma phagocytophilum, Ehrlichia muris, and "Candidatus Neoehrlichia mikurensis" determined in the Ixodes persulcatus ticks in the area of Urals, Siberia, and far east of Russia

A total of 3552 Ixodes persulcatus from Sverdlovsk, Chelyabinsk, Novosibirsk, Irkutsk regions and Khabarovsk Territory were examined on the Ehrlichia and Anaplasma presence by nested PCR based on the 16S rRNA gene. Both Anaplasma phagocytophilum and Ehrlichia muris DNA were found in I. persulcatus in all studied regions. A. Phagocytophilum was detected in 1.3-6.3% of ticks and E. muris - in 2.0-14.1% of ticks. Moreover, "Candidatus Neoehrlichia mikurensis" DNA was found in 8 ticks collected in Novosibirsk, Irkutsk Regions and Khabarovsk Territory. Partial nucleotide sequences of 16S rRNA gene and groESL operone (1240-1300 bp) were determined for 65 samples of A. Phagocytophilum, 17 samples of E. muris and 4 samples of "Candidatus Neoehrlichia mikurensis". Nucleotide sequences of 16S rRNA gene and groESL operone of E. muris and "Candidatus Neoehrlichia mikurensis" were shown to be highly conservative, and nucleotide sequences of groESL operone of both E. muris and "Candidatus Neoehrlichia mikurensis" differed from the sequences found previously in other species of Ixodid tick. On the basis of analysis of the 16S rRNA gene and groESL operone sequences it was concluded that all revealed samples A. Phagocytophilum could be divided into 2 groups. GroESL operone sequences of A. Phagocytophilum from the first group were identical to each other but significantly differed from the known groESL operone sequences (less than 98.2% of similarity), whereas their 16S rRNA gene sequences were identical to the sequence of widely distributed and pathogenic for human A. Phagocytophilum genetic variant (CAHU-HGEl, GenBank AF093788) or differed from it by a single nucleotide substitution. The nucleotide sequences of groESL operone of A. Phagocytophilum from the second group differed from each other by 1-4 nucleotides and were closely related (99.2-99.4% of similarity) to the sequences of groESL operone ofA. phagocytophilum isolates found in Europe in Ixodes ricinus and roe deer. The nucleotide sequences of the 16S rRNA gene of A. Phagocytophilum from the second group were most similar to the sequence of the rare A. Phagocytophilum genetic variant previously found only in China (GenBank DQ342324).     

A rat beta-interferon-induced mRNA: sequence characterization.

Polymerase chain reaction amplification of a cDNA derived from rat aortic smooth muscle cells, using sequences from conserved regions of the intramembrane domains of adrenergic receptors as primers, yielded the clone, rat8. This clone possesses a high degree of sequence similarity to a series of human interferon (IFN)-inducible genes. The rat8 sequence is 70% similar to that derived from the human alpha-IFN-induced gene, 9-27; there is 66% similarity between the deduced amino acid sequences encoded by the rat and the human genes. The rat homologue hybridizes with many bands in Southern analysis of rat DNA, suggesting that it is a member of a large multigene family.     

Purification and characterization of joining peptide and N-terminal peptide of proopiomelanocortin from the pars distalis of the bullfrog pituitary.

The joining peptide (JP) and the N-terminal peptide of proopiomelanocortin (NPP) were isolated from an acid-acetone extract of the distal lobe of the pituitary of the bullfrog, Rana catesbeiana, and purified by gel filtration and reverse-phase high performance liquid chromatography. The amino acid sequence of the bullfrog JP resembled the sequences of the JPs of Rana ridibunda (86% similarity) and Xenopus laevis (54% similarity), as deduced from the nucleotide sequences of their cDNAs. The amino acid sequence of bullfrog NPP showed 100%, 85%, and 50% similarity with those of Rana ridibunda, Xenopus laevis, and human NPPs, respectively. Administration of bullfrog NPP (0.05-5 micrograms/ml) to perifused Rana ridibunda interrenal slices induced a dose-dependent stimulation of corticosterone and aldosterone release. The present results indicate that the primary structure of NPP has been highly conserved during evolution. These data also reveal that NPP, which has no sequence homology with ACTH, exhibits a substantial corticotropic activity.     

Characterization and chromosomal organization of satellite DNA sequences in Picea abies

Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37-55 bp in length and had 68.9%-91.9% nucleotide sequence similarity. Two 2F repeats were 305-306 bp in length and had 83% sequence similarity. Two 3C repeats were 193-226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 x 106, 2.9 x 105, and 2.9 x 104, respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.     

Evidence that Xenopus laevis contains two different nonallelic insulin-like growth factor-I genes

Using the polymerase chain reaction (PCR), we have amplified and characterized partial nucleotide sequences of two distinct insulin-like growth factor-I genes (designated IGF-I' and IGF-I") from the amphibian, Xenopus laevis. The amplified fragments encoded much of the coding region of the mature peptide (exon III in mammalian IGF-I genes), and exhibited 93% similarity to each other, and 68-82% similarity to mammalian IGF-I amino acid sequences. Southern blot analysis using genomic DNA from a homozygous frog revealed that these two genes are nonallelic in a single organism, like the two nonallelic genes encoding Xenopus insulins that we have characterized previously. Furthermore, both IGF-I mRNAs are expressed in similar quantities in adult liver.     

中国淡水三角涡虫(Dugesia sp)的染色体研究(Ⅰ)

利用空气干燥法对不同产地淡水三角涡虫的染色体进行了研究。核型分析表明：河南淇县鱼泉三角涡虫(Dugesia sp)和浙江杭州龙井三角涡虫(Dugesia sp)体细胞中有16条染色体,为二倍体,核型公式为2n=2x=16=16m,均为具中部着丝粒染色体;河南济源不老泉三角涡虫(Dugesia sp)有24条染色体,为三倍体,核型公式为2n=3x=24=24m,亦全部由中部着丝粒染色体组成。上述3个产地淡水三角涡虫染色体的形态较为接近。北京樱桃沟三角涡虫(Dugesia sp)的体细胞染色体数目为24,为三倍体,核型公式为2n=3x=24=22m 2sm,由中部和亚中部着丝粒染色体组成,其中第2、4号各有一条染色体属于亚中部着丝粒染色体。研究结果表明：4个产地三角涡虫的体细胞染色体数目存在较大差异,包括二倍体(2n=2x=16)和三倍体(2n=3x=24),染色体基数属于x=8类型。     

Nucleotide sequence of a rabbit IgG heavy chain from the recombinant F-I haplotype

We report the sequence of a cDNA encoding a rabbit immunoglobulin gamma heavy chain of d12 and e14 allotypes with high homology to partial cDNA sequences from rabbits of d11 and e15 allotypes. The encoded rabbit protein shows homologies with human (68-70%) and mouse (60-63%) gamma chains. The nucleotide sequence homologies of the CH domains range from 76-84% with human and 64-76% with mouse sequences. Comparison of the portion of VH encoding amino acid positions 34-112 with a previously determined VH sequence of the same allotype shows high conservation of sequences in the second and third framework segments but more marked differences both in length and encoded amino acids of the second and third complementarity-determining regions (CDRs). We also found a high degree of homology with a human genomic V-region, VH26 (77%) and a remarkable similarity between rabbit and human second CDR sequences and human genomic D minigenes. These results provide additional evidence that D minigene sequences share information with the CDR2 portion of VH regions.