Site-directed gene integration in transgenic zebrafish mediated by cre recombinase using a combination of mutant Lox sites

With current gene-transfer techniques in fish, insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences, and multiple gene interactions make gene expression experiments difficult to interpret and fish phenotype less predictable. To meet different fish engineering needs, we describe here a gene targeting model in zebrafish. At first, four target zebrafish lines, each harboring a single genomic lox71 target site, were generated by zebrafish transgenesis. The zygotes of transgenic zebrafish lines were coinjected with capped Cre mRNA and a knockin vector pZklox66RFP. Site-specific integration event happened from one target zebrafish line. In this line two integrant zebrafish were obtained from more than 80,000 targeted embryos (integrating efficiency about 10(-4) to 10(-5)) and confirmed to have a sole copy of the integrating DNA at the target genome site. Genomic polymerase chain reaction analysis and DNA sequencing verified the correct gene target events where lox71 and lox66 have accurately recombined into double mutant lox72 and wild-type loxP. Each integrant zebrafish chosen for analysis harbored the transgene rfp at the designated egfp concatenates. Although the Cre-mediated recombination is site specific, it is dependent on a randomly placed target site. That is, a genomic target cannot be preselected for integration based solely on its sequence. Conclusively, an rfp reporter gene was successfully inserted into the egfp target locus of zebrafish genome by Cre-lox-mediated recombination. This site-directed knockin system using the lox71/lox66 combination should be a promising gene-targeting platform serving various purposes in fish genetic engineering.

attB site disruption in marine Actinomyces sp M048 via DNA transformation of a site-specific integration vector

An efficient conjugation method has been developed for the marine Actinomyces sp. isolate M048 to facilitate the genetic manipulation of the chandrananimycin biosynthesis gene cluster. A phi C31-derived integration vector pIJ8600 containing oriT and attP fragments was introduced into strain M048 by bi-parental conjugation from Escherichia coli ET12567 to strain M048. Transformation efficiency was (6.38 +/- 0.41) x 10(-5) exconjugants per recipient spore. Analysis of eight exconjugants showed that the plasmid pIJ8600 was stably integrated at a single chromosomal site (attB) of the Actinomyces genome. The DNA sequence of the attB was cloned and shown to be conserved. The results of antimicrobial activity analysis indicated that the insertion of plasmid pIJ8600 seemed to affect the biosynthesis of antibiotics that could strongly inhibit the growth of E. coli and Mucor miehei (Tu284). HPLC-MS analysis of the extracts indicated that disruption of the attB site resulted in the complete abolition of chandrananimycin A-C production, proving the identity of the gene cluster. Instead of chandrananimycins, two bafilomycins were produced through disruption of the attB site from the chromosomal DNA of marine Actinomyces sp. M048.

Gene transfer into genomes of human cells by the sleeping beauty transposon system

The Sleeping Beauty (SB) transposon system, derived from teleost fish sequences, is extremely effective at delivering DNA to vertebrate genomes, including those of humans. We have examined several parameters of the SB system to improve it as a potential, nonviral vector for gene therapy. Our investigation centered on three features: the carrying capacity of the transposon for efficient integration into chromosomes of HeLa cells, the effects of overexpression of the SB transposase gene on transposition rates, and improvements in the activity of SB transposase to increase insertion rates of transgenes into cellular chromosomes. We found that SB transposons of about 6 kb retained 50% of the maximal efficiency of transposition, which is sufficient to deliver 70-80% of identified human cDNAs with appropriate transcriptional regulatory sequences. Overexpression inhibition studies revealed that there are optimal ratios of SB transposase to transposon for maximal rates of transposition, suggesting that conditions of delivery of the two-part transposon system are important for the best gene-transfer efficiencies. We further refined the SB transposase to incorporate several amino acid substitutions, the result of which led to an improved transposase called SB11. With SB11 we are able to achieve transposition rates that are about 100-fold above those achieved with plasmids that insert into chromosomes by random recombination. With the recently described improvements to the transposon itself, the SB system appears to be a potential gene-transfer tool for human gene therapy.

RecA-mediated, targeted mutagenesis in zebrafish

We have evaluated the efficacy of RecA, a prokaryotic protein involved with homologous recombination, to direct site-specific mutagenesis in zebrafish embryos. For this we coinjected a vector containing a mutated enhanced green fluorescent protein (EGFP) gene plus 236-nucleotide corrective single-stranded DNAs coated with RecA into I-cell zebrafish embryos. Twenty-hours after fertilization, about 5% to 20% of injected embryos showed EGFP expression in I or more cells when RecA-coated corrective DNAs were used, but not when RecA was omitted. Mutated EGFP genes with 1-bp insertions or deletions were inefficiently activated, whereas those with 7-bp insertions were activated about 4-fold more efficiently. RecA-coated template strand had a higher efficiency than its complementary strand in activation of EGFP expression. Prior irradiation of the embryos with UV light enhanced RecA-mediated restoration of gene activity, suggesting that the effects we observed were augmented by one or more factors of zebrafish DNA repair systems.

Sleeping sites of Rhinopithecus bieti at Mt. Fuhe, Yunnan

Data on sleeping site selection were collected for a group of black-and-white snub-nosed monkeys (Rhinopithecus bieti; around 80) at Mt. Fuhe, Yunnan, China (99degrees20'E, 26degrees25'N, about 3,000 m asl) from November 2000 to January 2002. At the site mainly three vegetation types were present in an elevation-ascending order: deciduous broad leaf forest, mixed coniferous and broad leaf forest, and dark coniferous forest. In addition, bamboo forest presented in areas burned in 1958. Sleeping sites (n = 10) were located in the coniferous forest, where trees were the tallest, bottommost branches were the highest, the diameter of crowns was the second largest, and the gradient of the ground was the steepest. Monkeys usually kept quiet during entering and staying at a sleeping site. The site choice and the quietness may be tactics to avoid potential predators. In the coniferous forest, however, monkeys did not sleep in the valley bottom where trees were the largest, but frequently slept in the middle of the slope towards the east/southeast, in the shadow of ridges in three other directions, to avoid strong wind and to access sunshine; in winter-spring, they ranged in a more southern and lower area than in summer-autumn. These may be behavioral strategies to minimize energy stress in the cold habitat. Monkeys often slept in the same sleeping site on consecutive nights, which reflected a reduced pressure of predation probably due to either the effectiveness of anti-predation through sleeping site selection, or the population decline of predators with increasing human activities in the habitat. The group's behavioral responses to interactive and sometimes conflicting traits of the habitat are site-specific and conform to expectations for a temperate zone primate.

Free radical scavenging and antioxidant enzymes activation of polysaccharide extract from Nostoc sphaeroides

Nostoc sphaeroides Kuetzing has been used as a traditional medicine in China to treat a variety of ailments. This research identified the antioxidant activities of polysaccharide extract from Nostoc sphaeroides. The extract, which contains 46.2% carbohydrates, exhibited an effective scavenging capability on superoxide radical, hydroxyl radicals in non site-specific as well as site-specific assays, and also performed lipid peroxidation inhibition in a dose-dependent manner. Polysaccharide extract had no 1,1-diphenyl-2-picrylhydrazyl radical scavenging potential at all test concentrations. Activities of superoxide dismutase, catalase, and glutathione peroxidase in human embryo kidney 293 cells were increased effectively when Nostoc sphaeroides extract was applied. These results suggested that the use of N. sphaeroides in treating ailments may be based on the antioxidant capacities of polysaccharide composition.

Kinetic spectra of light-adaptation dark-adaptation and M-intermediate of BR-D96N

BR-D96N is a kind of genetically site-specific mutants of bacteriorhodopsin (BR) with obvious photochromic effect. Compared to the wild type BR, the lifetime of M state of BR-D96N is prolonged to several minutes so that the photochromic kinetics and the intermediates formation can be studied by the conventional spectra analysis. In the experiment, the absorption spectra of the sample at different time after light illumination are measured with spectrophotometer. By fitting and analyzing the variation of the spectra, we suppose that there are three main states in the, photochromic process, i.e., B state (light-adapted state), M state and D state (dark-adapted state). The absorption spectra of the B state, M state and D state are extracted from the experimental data based on this three-state model and the spectra at various time are fitted with the least-square method. So, the variations of population percentages of the M state, B state and D state are obtained and the M state and B state lifetimes are estimated. In another way, from the measurement of the absorption dynamics at 407 and 568 nm, the M state and B state lifetimes are also obtained by two exponential data fitting, which give coincident results with those of the spectra analysis. (C) 2003 Elsevier Science B.V. All rights reserved.

Photochromic kinetic spectra and intermediates of BR-D96N

BR-D96N is a kind of genetically site-specific mutant of bacteriorhodopsin (BR) with obvious photochromic effect. Compared to the wild type BR, the lifetime of M state of BR-D96N is prolonged to several minutes so that the photochromic kinetics and the intermediates formation can be studied by the conventional spectra analysis. In the experiment, the absorption spectra of the sample at different time after light illumination are measured with spectrophotometer. By fitting and analyzing the variation of the spectra, we suppose there-are three main states in the photochromic process, i.e. B state (light-adapted state), M state and D state (dark-adapted state). The absorption spectra of the B state, M state and D state are extracted from the experimental data based on this three-state model and the spectra at various time are fitted With the least square method. So, the variations of population percentages of the M state, B state and D state are obtained and the M state and B state lifetimes are estimated. In another,way, from measuring the absorption dynamics at 407 nm and 568 nm, the M state and B state lifetimes are also obtained by two exponential data fitting, which give coincident results with those of the spectra analysis.

5-氟尿嘧啶-β-环糊精结肠靶向前体药物的研究

5-氟尿嘧啶(5-Fluorouracil， 5-FU)是一种抗代谢药物，广泛用于临床治疗结直肠癌、胃癌、乳腺癌等多种癌症，但其首过代谢显著、亲脂性较低，选择性差、毒副作用大。为克服这些缺点人们对5-FU进行了大量的修饰工作，包括小分子修饰以及与各种载体形成微球、微囊、纳米粒、共价前药等。 环糊精(Cyclodextrin，简称CD)，可被结肠中的糖苷酶特异性地降解成小分子糖，而胃和小肠中由于缺乏相应的酶而使环糊精不被降解，这一特性在结肠药物的靶向输送及释放中有重要应用价值。环糊精中含有丰富的羟基，易进行化学修饰，将药物与环糊精通过共价键结合制成前药，使其在胃和小肠中不降解，而在盲结肠中被特异性的酶降解释出药物，达到结肠靶向释药的目的。研究表明，环糊精作为一种前药载体为结肠靶向释药和缓释、控释系统提供了一种有效的手段。 本工作选择5-氟尿嘧啶为模型药物、β-环糊精作为载体，通过中间体5-FU羧酸衍生物的制备及其与β-环糊精的偶联，合成了系列5-FU-β-CD前体药物，并利用紫外、红外、质谱、核磁、元素分析、热分析等手段对其进行结构表征。同时，还研究了前体药物的体外释药性质。具体内容包括： 1. 含有羧基的5-FU衍生物中间体的合成：(5-氟尿嘧啶-1-基)-乙酸(FUAC)、3-(5-氟尿嘧啶-1-基)-丙酸(FUPC)、5-(5-氟尿嘧啶-1-基)-戊酸(FUVC)的合成。 2. 中间体5-FU的羧酸衍生物与β-CD的偶联：分别通过以6-OTs-β-CD为中间体的取代法和活化酯法，合成了第一面取代和第二面取代的5-FU-β-CD大分子前体药物。在二面取代的前体药物制备中，通过改变原料的比例，合成了系列不同取代度(DS)的2-[(5-氟尿嘧啶-1-基)-乙酰基] -β-环糊精结合物。 3. 对上述前体药物进行体外释放研究：分别考察了前体药物在不同pH缓冲溶液中的水解行为及其在小鼠胃肠道人工体液中的酶解行为，并通过UV-Vis及HPLC对前体药物释放情况进行检测分析。 5-Fluorouracil(5-Fu), commonly known as a broad-spectrum antineoplastic drug, has been widely used in the treatment of various kinds of cancer including colon cancer for 40 years. However, this antitumor agent exhibits serious adverse effects, such as their marrow toxicity, gastrointestinal reaction and low selectivity in their clinical use. In order to improve its antitumor activity and reduce its toxicity, the compound was modified in various ways, including the formation of conjugated prodrugs with kinds of carrier, microsphere and nanoparticles etc. Cyclodextrins(CDs) are known to be barely capable of being hydrolyzed and only slightly absorbed in passing through the stomach and small intestine; however they are fermented into small saccharides by colonic microflora and thus absorbed as small saccharides in the large intestine. This biodegradation property of CDs may be useful as a colon-targeting carrier, and thus CD prodrugs may serve as a source of site-specific delivery of drugs to colon. It was demonstrated that prodrugs of CDs can provide a versatile means for construction of not only colon targeted delivery systems, but also delayed release systems. 5-Fluorouracil was taken as a model drug and β-CD as the carrier in this study. Series prodrugs of 5-FU was prepared through the preparation of reactive 5-FU derivatives containing carboxyl group and coupling to hydroxyl groups of CD. The structures of the conjugates were charactered by using IR, UV–vis, ESI-MS, 1H, 13C-NMR spectra, elemental analyses, and thermal analysis. In vitro hydrolysis behavior in aqueous solution and in rat gastrointestinal tract contents of the conjugates were also investigated. The main content of this dissertation includes following aspects: 1. The preparation of 5-FU derivatives containing carboxyl group: 5-Fluorouracil- acetic acid(FUAC)、3-(5-FU-1)-propionic acid (FUPC)、and 5-(5-FU-1)-valeric acid(FUVC). 2. The coupling of 5-FU derivatives to β-CD: 5-FU was selectively conjugated onto the primary or secondary hydroxyl groups of β-CD through an ester linkage, by the substitution of 6-OTs-β-CD and the activated ester method respectively. For the secondary face conjugation, the degree of substitution(DS) can be controlled by changing the mole ratio of the starting materials(FUAC and β-CD). 3. In vitro release behavior of the conjugates in aqueous solution and in rat gastro- intestinal tract contents of the conjugates were investigated, and the reaction was monitored and analyzed by using UV-Vis and HPLC methods.

川西亚高山针叶林主要针叶树种年轮生态学研究

米亚罗地区是四川西部较为典型的亚高山针叶林区域之一。为建立该地区主要针叶树种岷江冷杉、云杉、紫果云杉和红杉的年轮宽度年表资料，了解不同海拔高度岷江冷杉原始林和不同恢复过程的人工针叶林及次生混交林树木径向生长规律，结合样地调查，用生长锥钻取了树木芯样做年轮生态学分析。芯样经过标准化程序固定和打磨抛光后，用WinDENDRO图像分析系统测量年轮宽度序列，用COFECHA程序交叉定年和控制测量数据质量，用ARSTAN程序建立了4个主要针叶树种的地区年表和不同海拔高度岷江冷杉林及人工针叶林和次生混交林针叶树的样地年表。 4个主要针叶树种年轮宽度年表的平均敏感度低于0.2，而其晚材宽度年表都具相对较高的平均敏感度。早材宽度与年轮总宽度标准化年表间的相关系数均在0.9以上；晚材宽度与年轮总宽度标准化年表间的相关系数则种间差异较大，红杉的最高，岷江冷杉的最低。岷江冷杉晚材宽度与年轮总宽度的相关性从1970年以后明显下降，而其他种的相关系数则随时间变化较小。树种之间标准化年表显著正相关，而云杉与紫果云杉和红杉与岷江冷杉之间相关系数明显较高。年表序列的第1主分量表达了4个树种树木共同径向生长变化格局；第2至第4主分量分别表达了云杉属和冷杉属、常绿针叶树种和落叶针叶树种以及云杉和紫果云杉树木径向生长变化差异。 不同海拔高度的8个岷江冷杉样地年轮宽度年表序列敏感度大体上随海拔高度升高而降低。各样地早材宽度与年轮总宽度年表之间的相关系数均在0.9以上，且随海拔高度变化不大；晚材宽度与年轮总宽度之间的相关系数随海拔高度的变化较大，并有随海拔升高而降低的趋势。样地年表序列之间相关系数差异很大，高海拔样地年表间多为显著正相关；低海拔样地年表间的相关系数变化不一；高海拔和低海拔样地年表之间相关性较差，且多不显著。样地年表的第1主分量能解释年表序列总方差的37.5%，反映了不同海拔高度岷江冷杉林木共同的径向生长变化格局；第2和第3主分量分别解释总方差的24.5%和18.2%，表现出明显的高海拔和低海拔样地树木间不同的径向生长变化，除一些样地例外，它们一般与低海拔样地年表有正相关，与高海拔样地年表有负相关。在那些另外的样地，海拔以外的其他因素可能也影响了树木径向生长变化。不同海拔高度样地林木的生长抑制和生长释放频率在不同时期表现出较大的差异，表明了不同的干扰历史和林木补充时间。 人工针叶林和次生混交林各样地林木早材宽度与其年轮总宽度年表之间相关系数均高达0.9以上；晚材宽度与年轮总宽度年表之间也都显著正相关，但人工针叶林样地的明显较高。样地年表序列之间的相关关系表现为，林分起源和经营管理相似的样地年表之间的相关系数明显较高，如人工针叶林与人工针叶林尽管树种不同，但样地年表之间显著正相关，而与次生混交林样地年表间关系不显著；反之亦然。综合比较各项生长参数及不同时期的树木径向生长速率，人工针叶林树木的胸径增长至少在40年以内是优于次生混交林的同种（或不同种）针叶树的。不同样地林木生长释放和生长抑制及人工针叶林树木胸高断面积增长分析表明，除严重的人为干扰外，林分郁闭后林木密度过大是造成高频率生长抑制的主要原因，在林分发育的适当时期通过抚育间伐等措施调控林分密度，是保证林木胸高断面积在一定时期内保持较高的连年增长的关键。日本落叶松作为引进的树种，在海拔3100 m左右种植表现良好，近30年来各项生长指标均高于林龄相近的云杉人工林，因此，适当用其作为川西亚高山针叶林采伐迹地快速恢复是合理的。 Miyaluo area is one of the typical regions covered by subalpine coniferous forests in western Sichuan province of southwestern China. To develop the regional tree-ring width chronology series for the dominant conifers such as Abies faxoniana, Picea asperata, P. purpurea and Larix potaninii, and to understand the radial growth patterns of conifers in Abies faxoniana natural forest stands at different altitudes, and in coniferous plantations and natural regenerated mixed stands in their different restoring processes as well, increment cores were sampled in the field together with conventional plots investigations for dendroecological analyses. After the increment cores being prepared according to standard procedures, the ring widths (total-ring and intra-ring widths) were measured with a WinDENDRO image-analysis system, and the measured tree-ring sequences were crossdated and quality-controlled with the software COFECHA. Using the software ARSTAN, we developed tree-ring width based chronology series of the four dominant conifers, eight site-specific Abies faxoniana chronologies, and seven site-specific chronologies of conifers in coniferous plantations and natural regenerated mixed stands. Mean sensitivities for total ring width chronologies of the four sampled dominant conifers were all below 0.2, while those for the latewood width chronologies of the same species were relatively much higher. Correlation coefficients between standard earlywood and total ring width chronologies of the four conifers were all above 0.9, but those between standard latewood and total ring width chronologies exhibited differences among species, with the coefficient of Larix potaninii the highest and that of Abies faxoniana the lowest. Correlation coefficients between latewood and total ring width of A. faxoniana obviously decreased from 1920-1970 for successive 50-year segments with 10-years lag analyses, though the same for the other three species changed unnoticeably with time. Tree-ring standard chronologies among species showed significant positive correlations, with the correlation coefficients between chronologies of Picea asperata and P. purpurea, and of Larix potaninii and Abies faxoniana relatively much higher. The first principal component of tree-ring chronologies represented the common radial growth patterns of the four conifers in Miyaluo area. The second, third and fourth PCs expressed the differences in radial growth responses for the genus Picea and Abies, for the evergreen and deciduous confers, and for the two species of the genus Picea, respectively. In general, mean sensitivities of the eight Abies faxoniana site-specific tree-ring width chronologies decreased with increasing altitude. The correlation coefficients between earlywood and total ring width chronologies for all sites reached 0.9, which did not change much with altitude; but those between latewood and total ring width chronologies diversified, with a decreasing tendency from lower altitudinal sites to higher altitudinal sites. Correlation coefficients among site chronologies varied considerably, with significant positive correlations among higher site chronologies, mixed results among lower site chronologies, and poor and insignificant correlations between chronologies of higher site and lower site. The first PC, which represents 37.5% of the total variance, reflected a common radial growth response at sites of different altitudes, and it showed a tendency of explaining more variance with increasing altitude. The second and the third PCs contributed to 24.5% and 18.2% of the total variance, respectively, exhibiting distinctive differences in radial growth responses between low- and high-altitudinal sites. With some exceptions, the radial growth represented by the second and third PCs had a positive correlation with that at the low-altitudinal sites and a negative correlation with that at the high-altitudinal sites. For those exceptional sites, factors other than altitude might also play a role in affecting tree-ring growth variations. Trees in stands of different altitudes showed great differences in frequencies of growth suppressions and releases through times, suggesting different disturbance histories and periods when trees recruiting to the canopy. Correlation coefficients between earlywood and total ring width chronologies for all sites of coniferous plantations and natural regenerated mixed stands were also above 0.9; and the same between latewood width and total ring width chronologies all positively correlated, too, with the coefficients of the coniferous plantations obviously much higher. Correlations among site chronologies showed that the coefficients among sites with similar stand origin and management regimes were much higher than those among sites with different stand origin and management regimes. For example, significant positive correlations were found for chronologies among different coniferous plantations, irrespective of species differences; while insignificant correlations between chronologies of the same conifer from a coniferous plantation and a natural regenerated mixed stand, and vise versa. Integrative comparisons of different tree growth parameters and radial growth rates at different stages indicated that the diameter at breast height (DBH) increments for trees in coniferous plantations were faster than those for trees of the same (or different) species in the natural regenerated mixed stands, at least within their first 40 years of stand development. Analyses of growth releases and suppressions, and basal area increments of trees in different stands demonstrated that over-dense individuals after canopy closure was the main factor resulting in high frequencies of radial growth suppressions, with some exceptions of severe man-made disturbances. Therefore, to ensure a continuous basal area current annual increment in certain periods, tree density controlling through thinning in due time during the stand development process are necessary. It should be mentioned that, as an introduced conifer to Miyaluo area, Larix kaempferi grew quite well at altitude of ca. 3100 m after planting in 1970s. In their near 30 years of stand development, Larix kaempferi trees exhibited faster growth in various parameters than Picea asperata trees of the similar stand age did. Thus we think it reasonable to use Larix kaempferi as a fast restoring species at appropriate sites of cutting blanks of subalpine coniferous forests in western Sichuan.

Direct patterning of rhodamine 6G molecules on mica by dip-pen nanolithography

Dip-pen nanolithography (DPN) has been developed to pattern monolayer film of various molecules on suitable substrate through the controlled movement of ink-coated atomic force microscopy (AFM) tip, which makes DPN a potentially powerful tool for making the functional nanoscale devices. In this paper, the direct patterning of rhodamine 6G on mica by dip-pen nanolithography was demonstrated. R6G features patterned on the mica was successfully achieved with different tip movement which can be programmed by Nanoscript(TM) language. From the AFM image of R6G patterns, we know that R6G molecule is flatly binding to the mica surface through electrostatic interaction, thus stable R6G nanostructures could be formed on mica. The influence of translation speed and contact time on DPN was discussed. The method can be extended to direct patterning of many other organic molecules, and should open many opportunities for miniaturized optical device and site-specific biological staining.

Responses of vegetative gametophytes of Undaria pinnatifida to high irradiance in the process of gametogenesis

The population of Undaria pinnatifida in its ecologic niche sustains itself in high temperature summer in the form of vegetative gametophytes, the haploid stage in its heteromorphic life cycle. Gametogenesis initiates when seawater temperature drops below the threshold levels in autumn in the northern hemisphere. Given that the temperature may fall into the appropriate range for gametogenesis, the level of irradiance determines the final destiny of a gametophytic cell, either undergoing vegetative cell division or initiating gametogenesis. In elucidating how vegetatively propagated gametophytes cope with changes of irradiance in gametogenesis, we carried out a series of culture experiments and found that a direct exposure to irradiance as high as 270 mu mol photons m(-2) s(-1) was lethal to dim-light (7-10 mu mol photons m(-2) s(-1)) adapted male and female gametophytes. This lethal effect was linearly corelated with the exposure time. However, dim-light adapted vegetative gametophytes were shown to be able tolerate as high as 420 mu mol photons m(-2) s(-1) if the irradiance was steadily increased from dim light levels (7-10 mu mol photons m(-2) s(-1)) to 90, 180 and finally 420 mu mol photons m(-2) s(-1), respectively, at a minimum of 1-3 h intervals. Percentage of female gametophytic cells that turned into oogonia and were eventually fertilized was significantly higher if cultured at higher but not lethal irradiances. Findings of this investigation help to understand the dynamic changes of population size of sporophytic plants under different light climates at different site-specific ecologic niches. It may help to establish specific technical details of manipulation of light during mass production of seedlings by use of vegetatively propagated gametophytes.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.