RNA-Seq reveals virus–virus and virus–plant interactions in nature

As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus–virus and virus–host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus. Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1. Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant–virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications

A novel superior factor widely controlling the rice grain quality

Synthesis of storage starch and protein accumulation is the main action of endosperm organogenesis in term of the economic importance of rice. This event is strongly disturbed by abiotic stresses such as high temperature; thus, the upcoming global warming will cause a crisis with a great impact on food production^1,2^. The enzymes for the protein storage and starch synthesis pathway should work in concert to carry out the organogenesis of rice endosperm^3-5^, but the regulatory mechanism is largely unknown. Here we show that a novel regulatory factor, named OsCEO1, acts as the conductor of endosperm organogenesis during the rice grain filling stage. The physiological properties of _floury-endosperm-2_ (_flo2_) mutants showed many similarities to symptoms of grains developed under high-temperature conditions, suggesting important roles of the responsible gene in sensitivity to high-temperature stress. Our map-based cloning identified the responsible gene for the _flo2_ mutant, _OsCEO1_, which has no homology to any genes of known function. The _OsCEO1_ belongs to a novel conserved gene family and encodes a protein composed of 1,720 amino acid residues containing a TPR (tetratricopeptide repeat) motif, which is considered to mediate a protein-protein interaction. The yeast two-hybrid analysis raised an unknown protein showing homology to a late embryogenesis abundant protein and a putative basic helix-loop-helix protein as candidates for the direct interactor for _OsCEO1_, whereas no enzyme genes for the synthesis of storage substances were detected. The _flo2_ mutant exhibited reduced expression of several genes for putative regulatory proteins as well as many enzymes involved in storage starch and proteins. These results suggest that _OsCEO1_ is a superior conductor of the novel regulatory cascade of endosperm organogenesis and may have important roles in the response to high-temperature stress

ダイ49ジ ナンキョク チイキ カンソクタイ ナツタイ ニオケル コショウ カンソク

第49次日本南極地域観測隊(第49次)夏隊において,湖沼観測として湖沼環境観測,生物・生態学的研究試料としての湖水と湖底の生物群集採取,及び現場実験を宗谷海岸露岩域にある複数の湖沼で実施した.この湖沼観測報告は南極観測事業第VII期計画の一般プロジェクト研究(P3)「極域環境変動と生態系変動に関する研究」及びモニタリング研究観測(M4)「生態系変動のモニタリング」の両課題にかかわる観測を記録したものである.野外観測は2007年12月22日から2008年2月13日の期間,砕氷船「しらせ」が昭和基地沖近傍に滞在中に実施した.今回は夏季の湖沼環境変動と湖底の生物(藻類群集)の応答を集中的に観測すべく,スカルブスネスの長池にて観測とサンプリング・現場実験を繰り返し実施する一方,きざはし浜生物観測小屋から徒歩日帰り圏内にある周辺の14湖沼,及びヘリコプターを利用した日帰り観測にてスカルブスネス東部の4湖沼,及び他の露岩,スカーレンにあるスカーレン大池,ラングホブデ域の雪鳥池・東雪鳥池,ぬるめ池にて湖沼水質環境観測と試料採集を適宜実施した.このうち,スカルブスネス東部のなまず池 (仮称)では潜水による水中設置ビデオ装置の回収と,湖底のコケ類・藻類が作り上げている「とさか・筍状」の群落の採集,ラングホブデぬるめ池では湖底から小型カイアシ類の定量サンプリングを実施,これらを研究試料として日本に持ち帰ることができた.また,第47次隊により雪の堤防の決壊の発見(第46次越冬期間中に決壊したとみられる)が報告されたラングホブデ南部の平頭氷河末端にあった「氷河池」(仮称)の現状視察も実施,決壊前後での3m以上と思われる大幅な水位変動痕からフィルム状の生物試料を採集し持ち帰った.Observations on the limnological properties, samplings of waters and bottom assemblages for biological and ecological studies, and some field experimental studies at several lakes in Soya Coast ice-free areas, were carried out during the austral summer season in the 49th Japanese Antarctic Research Expedition (JARE), 2007-2008. These studies were planned as one of the research projects named, "Studies on the changes of polar environments and ecosystems (P-3)" and the monitoring studies named "Monitoring for ecosystems (M-4)" during the 7th term of the Japanese Antarctic Research Expedition Plans. Field studies were done from 22 December 2007 to 13 February 2008, while our Ice Breaker Shirase stayed at/near off Syowa Station. To clarify the relationships among seasonal changes of environmental factors and biological responses, frequent field observations were performed at Naga Ike, one of the freshwater lakes in the Skarvsnes ice-free area. General limnological and biological samplings at the other lakes in the area (14 lakes near the Kizahasi Beach field base camp) were also done during the term. Observations and samplings distant from the base camp, four lakes in eastern Skarvsnes, a lake in Skallen, and three lakes in Langhovde, were also done using a helicopter for transportation. From Namazu Ike (temporary name) in eastern Skarvsnes, submersible video cameras were retrieved and so-called `algal crest\u27, benthic moss-algal assemblages, were sampled by scuba diving. Benthic copepods were sampled quantitatively from Nurume Ike in Langhovde. From Hyoga Ike (temporary name), a snow-dammed glacial lake which lost its water by recent breakage (during the JARE-46 wintering period), thin bio-film samples were collected from the present lake shore formerly part of the lake bed

Results of the search for inspiraling compact star binaries from TAMA300's observation in 2000-2004

We analyze the data of TAMA300 detector to search for gravitational waves from inspiraling compact star binaries with masses of the component stars in the range 1-3Msolar. In this analysis, 2705 hours of data, taken during the years 2000-2004, are used for the event search. We combine the results of different observation runs, and obtained a single upper limit on the rate of the coalescence of compact binaries in our Galaxy of 20 per year at a 90% confidence level. In this upper limit, the effect of various systematic errors such like the uncertainty of the background estimation and the calibration of the detector's sensitivity are included.Comment: 8 pages, 4 Postscript figures, uses revtex4.sty The author list was correcte

Observation results by the TAMA300 detector on gravitational wave bursts from stellar-core collapses

We present data-analysis schemes and results of observations with the TAMA300 gravitational-wave detector, targeting burst signals from stellar-core collapse events. In analyses for burst gravitational waves, the detection and fake-reduction schemes are different from well-investigated ones for a chirp-wave analysis, because precise waveform templates are not available. We used an excess-power filter for the extraction of gravitational-wave candidates, and developed two methods for the reduction of fake events caused by non-stationary noises of the detector. These analysis schemes were applied to real data from the TAMA300 interferometric gravitational wave detector. As a result, fake events were reduced by a factor of about 1000 in the best cases. The resultant event candidates were interpreted from an astronomical viewpoint. We set an upper limit of 2.2x10^3 events/sec on the burst gravitational-wave event rate in our Galaxy with a confidence level of 90%. This work sets a milestone and prospects on the search for burst gravitational waves, by establishing an analysis scheme for the observation data from an interferometric gravitational wave detector

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Complete genome sequence of a novel partitivirus from a wild brassicaceous plant, Arabidopsis halleri

Two contigs with high similarity to partitivirus sequences were identified by de novo assembly of sequences obtained by RNA-Seq from a wild brassicaceous plant, Arabidopsis halleri subsp. gemmifera. Here, we report the complete genome sequence of a putative novel partitivirus. Excluding the poly-A tail, it consists of two RNA genome segments of 1912 and 1769 bp, which are predicted to encode a 585-amino-acid-long putative RNA-dependent RNA polymerase (RdRp) and a 487-amino-acid-long putative capsid protein (CP), respectively. Phylogenetically, this virus belongs to the genus Alphapartitivirus and is most closely related to Raphanus sativus partitivirus 1 from radish. We propose the name "Arabidopsis halleri partitivirus 1" (AhPV1) for this novel virus

RNA-Seq reveals virus–virus and virus–plant interactions in nature

As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus–virus and virus–host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus. Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1. Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant–virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications

A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq

Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses