Identification of a DNA nonhomologous end-joining complex in bacteria

In eukaryotic cells, double-strand breaks (DSBs) in DNA are generally repaired by the pathway of homologous recombination or by DNA nonhomologous end joining (NHEJ). Both pathways have been highly conserved throughout eukaryotic evolution, but no equivalent NHEJ system has been identified in prokaryotes. The NHEJ pathway requires a DNA end-binding component called Ku. We have identified bacterial Ku homologs and show that these proteins retain the biochemical characteristics of the eukaryotic Ku heterodimer. Furthermore, we show that bacterial Ku specifically recruits DNA ligase to DNA ends and stimulates DNA ligation. Loss of these proteins leads to hypersensitivity to ionizing radiation in Bacillus subtilis. These data provide evidence that many bacteria possess a DNA DSB repair apparatus that shares many features with the NHEJ system of eukarya and suggest that this DNA repair pathway arose before the prokaryotic and eukaryotic lineages diverged.     

DNA干扰现象及其作用机理研究进展

与体内某一基因相同的DNA序列可特异性抑制细胞内靶标基因的表达,这种现象称之为DNA干扰(DNAi)。DNAi是随着转录后基因沉默现象而在烟草属植物上被发现,之后在一些动植物及其细胞上也被发现。在原核生物中也存在DNAi现象,且原核生物的Ago在体外也能实现DNAi。原核生物DNAi的机理主要是Ago以DNA为向导切割DNA或RNA,而真核生物可能是基因转录后抑制、基因组甲基化和启动子结合的转录抑制等。本文还对DNAi的进一步研究和应用进行了讨论和展望。     

The origins of genome complexity

Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.     

Remote sensing of ocean currents

A method of remotely measuring near-surface ocean currents with a synthetic aperture radar (SAR) is described. The apparatus consists of a single SAR transmitter and two receiving antennas. The phase difference between SAR image scenes obtained from the antennas forms an interferogram that is directly proportional to the surface current. The first field test of this technique against conventional measurements gives estimates of mean currents accurate to order 20 percent, that is, root-mean-square errors of 5 to 10 centimeters per second in mean flows of 27 to 56 centimeters per second. If the full potential of the method could be realized with spacecraft, then it might be possible to routinely monitor the surface currents of the world's oceans.     

Anthropogenic CO2 uptake by the ocean based on the global chlorofluorocarbon data set

We estimated the oceanic inventory of anthropogenic carbon dioxide (CO2) from 1980 to 1999 using a technique based on the global chlorofluorocarbon data set. Our analysis suggests that the ocean stored 14.8 petagrams of anthropogenic carbon from mid-1980 to mid-1989 and 17.9 petagrams of carbon from mid-1990 to mid-1999, indicating an oceanwide net uptake of 1.6 and 2.0 +/- 0.4 petagrams of carbon per year, respectively. Our results provide an upper limit on the solubility-driven anthropogenic CO2 flux into the ocean, and they suggest that most ocean general circulation models are overestimating oceanic anthropogenic CO2 uptake over the past two decades.     

The effects of iron fertilization on carbon sequestration in the Southern Ocean

An unresolved issue in ocean and climate sciences is whether changes to the surface ocean input of the micronutrient iron can alter the flux of carbon to the deep ocean. During the Southern Ocean Iron Experiment, we measured an increase in the flux of particulate carbon from the surface mixed layer, as well as changes in particle cycling below the iron-fertilized patch. The flux of carbon was similar in magnitude to that of natural blooms in the Southern Ocean and thus small relative to global carbon budgets and proposed geoengineering plans to sequester atmospheric carbon dioxide in the deep sea.     

Bacterial taxa that limit sulfur flux from the ocean

Flux of dimethylsulfide (DMS) from ocean surface waters is the predominant natural source of sulfur to the atmosphere and influences climate by aerosol formation. Marine bacterioplankton regulate sulfur flux by converting the precursor dimethylsulfoniopropionate (DMSP) either to DMS or to sulfur compounds that are not climatically active. Through the discovery of a glycine cleavage T-family protein with DMSP methyltransferase activity, marine bacterioplankton in the Roseobacter and SAR11 taxa were identified as primary mediators of DMSP demethylation to methylmercaptopropionate. One-third of surface ocean bacteria harbor a DMSP demethylase homolog and thereby route a substantial fraction of global marine primary production away from DMS formation and into the marine microbial food web.     

重庆稻瘟病菌群体遗传多样性分析

采用rep-PCR指纹技术,对73个重庆稻瘟病菌菌株进行了DNA指纹扩增。结果表明,菌株间显示了DNA指纹的多态性,供试菌株分别扩增出2~17条DNA带。经UPGMA聚类分析,在0.80遗传相似水平下,供试菌株分为12个遗传谱系,其中谱系L7,L9,L12为优势谱系。重庆稻瘟病菌的群体结构呈现多样性和复杂性,菌株的遗传谱系与原寄主品种和地理分布之间均表现出较明显的相关性。     

Vertical nitrate fluxes in the oligotrophic ocean

The vertical flux of nitrate across the thermocline in the upper ocean imposes a rigorous constraint on the rate of export of organic carbon from the surface layer of the sea. This export is the primary means by which the oceans can serve as a sink for atmospheric carbon dioxide. For the oligotrophic open ocean regions, which make up more than 75% of the world's ocean, the rate of export is currently uncertain by an order of magnitude. For most of the year, the vertical flux of nitrate is that due to vertical turbulent transport of deep water rich in nitrate into the relatively impoverished surface layer. Direct measurements of rates of turbulent kinetic energy dissipation, coupled with highly resolved vertical profiles of nitrate and density in the oligotrophic eastern Atlantic showed that the rate of transport, averaged over 2 weeks, was 0.14 (0.002 to 0.89, 95% confidence interval) millimole of nitrate per square meter per day and was statistically no different from the integrated rate of nitrate uptake as measured by incorporation of (15)N-labeled nitrate. The stoichiometrically equivalent loss of carbon from the upper ocean, which is the relevant quantity for the carbon dioxide and climate question, is then fixed at 0.90 (0.01 to 5.70) millimole of carbon per square meter per day. These rates are much lower than recent estimates based on in situ changes in oxygen over annual scales; they are consistent with a biologically unproductive oligotrophic ocean.     

重庆稻瘟病菌不同菌株DNA指纹图谱分析

采用rep-PCR指纹技术对70个不同来源的稻瘟病菌菌株的DNA指纹图谱进行了测定。菌株间显示了DNA图像的多态性,供试菌株分别扩增出2－15条DNA带。经聚类分析,在0．80遗传相似水平下,供试菌株分为9个遗传谱系,其中第3,6,9为优势谱系。菌株的遗传谱系与菌株的原寄主和原采集地之间均表现出较明显的相关性。     

The Southern Ocean's role in carbon exchange during the last deglaciation

Changes in the upwelling and degassing of carbon from the Southern Ocean form one of the leading hypotheses for the cause of glacial-interglacial changes in atmospheric carbon dioxide. We present a 25,000-year-long Southern Ocean radiocarbon record reconstructed from deep-sea corals, which shows radiocarbon-depleted waters during the glacial period and through the early deglaciation. This depletion and associated deep stratification disappeared by ~14.6 ka (thousand years ago), consistent with the transfer of carbon from the deep ocean to the surface ocean and atmosphere via a Southern Ocean ventilation event. Given this evidence for carbon exchange in the Southern Ocean, we show that existing deep-ocean radiocarbon records from the glacial period are sufficiently depleted to explain the ~190 per mil drop in atmospheric radiocarbon between ~17 and 14.5 ka.     

2000和2001年江苏省稻瘟病菌的群体结构

利用Pot2-rep-PCR技术分析了2000及2001年采自江苏省五大稻区稻瘟病菌的DNA指纹。单元型和系谱分析结果表明：稻瘟病菌在DNA水平上具有很高的多态性；不同的年份及地区间稻瘟病菌的群体结构存在明显差异，但也有部分菌株属于相同系谱甚至同一单元型，而JSL17是各稻区均有分布的优势系谱；来自不同地区、相同寄主品种的菌株有相似的遗传背景，说明寄主品种的遗传背景在病菌进化的变异中起着重要的作用。     

贵州稻瘟病菌群体的遗传多样性初步研究

采用Rep—PCR分子指纹技术对2003～2005年采自贵州省内的稻瘟病菌Magnaporth grisea菌株进行DNA指纹分析,结果显示,200个供试菌株分别扩增到2～15条DNA带,经UPGMA聚类分析,在0．774遗传相似水平下,供试菌株划分为19个遗传谱系,141个单元型。优势谱系为GZL7和GZL6,分别拥有49个和26个单元型,其菌株分别占42％和20．5％。研究显示,贵州稻瘟病菌的群体结构呈现多样性和复杂性,同时揭示菌株的遗传谱系与品种和生理环境有明显的相关性。     

Independent and parallel recruitment of preexisting mechanisms underlying C₄ photosynthesis

C? photosynthesis allows increased photosynthetic efficiency because carbon dioxide (CO?) is concentrated around the key enzyme RuBisCO. Leaves of C? plants exhibit modified biochemistry, cell biology, and leaf development, but despite this complexity, C? photosynthesis has evolved independently in at least 45 lineages of plants. We found that two independent lineages of C? plant, whose last common ancestor predates the divergence of monocotyledons and dicotyledons about 180 million years ago, show conserved mechanisms controlling the expression of genes important for release of CO(2) around RuBisCO in bundle sheath (BS) cells. Orthologous genes from monocotyledonous and dicotyledonous C? species also contained conserved regulatory elements that conferred BS specificity when placed into C? species. We conclude that these conserved functional genetic elements likely facilitated the repeated evolution of C? photosynthesis.     

Small phytoplankton and carbon export from the surface ocean

Autotrophic picoplankton dominate primary production over large oceanic regions but are believed to contribute relatively little to carbon export from surface layers. Using analyses of data from the equatorial Pacific Ocean and Arabian Sea, we show that the relative direct and indirect contribution of picoplankton to export is proportional to their total net primary production, despite their small size. We suggest that all primary producers, not just the large cells, can contribute to export from the surface layer of the ocean at rates proportional to their production rates.     

Temporal relationships of carbon cycling and ocean circulation at glacial boundaries

Evidence from high-sedimentation-rate South Atlantic deep-sea cores indicates that global and Southern Ocean carbon budget shifts preceded thermohaline circulation changes during the last ice age initiation and termination and that these were preceded by ice-sheet growth and retreat, respectively. No consistent lead-lag relationships are observed during abrupt millennial warming events during the last ice age, allowing for the possibility that ocean circulation triggered some millenial climate changes. At the major glacial-interglacial transitions, the global carbon budget and thermohaline ocean circulation responded sequentially to the climate changes that forced the growth and decline of continental ice sheets.     

四川稻瘟病菌遗传宗谱的地理分布及与寄主品种的相关性研究

本研究应用rep-PCR分子指纹技术,对2000~2002年采自四川6个自然生态稻作区的137个稻瘟病菌菌株进行了DNA指纹谱型分析。以0.19遗传相似水平将供试菌株划分成37个遗传宗谱,层次较为丰富。结果表明,各稻作区稻瘟病菌遗传宗谱丰富,它们既有相同的遗传宗谱(即宗谱SCL36、37),又具有自己的特异性宗谱。在杂交稻和常规稻上检测出8个共同稻瘟病菌遗传宗谱,表明它们之间具有一定的亲缘关系;不同的宗谱在杂交稻与常规稻上的分布存在差异,有着自己的优势寄主。     

The ocean: a natural source of carbon monoxide

The surface waters of the western Atlantic are supersaturated with respect to the partial pressure of carbon monoxide in the atmosphere. Under these conditions, the net transport of carbon monoxide across the air-sea interface must be from the sea into the atmosphere. Thus, the ocean appears to act as a source of carbon monoxide. The ocean may be the largest known natural source of this gas, contributing possibly as much as 5 percent of the amount generated by burning of fuels by man.     

Carbon isotope constraints on the deglacial CO₂ rise from ice cores

The stable carbon isotope ratio of atmospheric CO(2) (δ(13)C(atm)) is a key parameter in deciphering past carbon cycle changes. Here we present δ(13)C(atm) data for the past 24,000 years derived from three independent records from two Antarctic ice cores. We conclude that a pronounced 0.3 per mil decrease in δ(13)C(atm) during the early deglaciation can be best explained by upwelling of old, carbon-enriched waters in the Southern Ocean. Later in the deglaciation, regrowth of the terrestrial biosphere, changes in sea surface temperature, and ocean circulation governed the δ(13)C(atm) evolution. During the Last Glacial Maximum, δ(13)C(atm) and atmospheric CO(2) concentration were essentially constant, which suggests that the carbon cycle was in dynamic equilibrium and that the net transfer of carbon to the deep ocean had occurred before then.