The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Culture potential of Amblypharyngodon mola with carps in polyculture in farmers' pond of northern regions of Bangladesh

To assess the culture potential of mola (Amblypharyngodon mola) along with carps in polyculture systems, an experiment consisted of three treatments each with five replications was conducted for 4 months in two villages of Parbatipur upazilla under Dinajpur district. In the first treatment (SS), catla, rohu, mrigal, grass carp, Thai punti, common carp and a higher density of silver carp (8 per 40m²) were stocked. In the second treatment (SM), stocking density of silver carp was reduced to half and mola was added at a stocking density of 12,500/ha with all other fishes used in SS. In the third treatment (MM), no silver carp was stocked and mola was added at a stocking density of 25,000/ha with all other fishes used in SS. All treatments were subjected to the same regime of feed and fertilizers. The yields of large carps were 2035 kg/ha, 1757 kg/ha and 1326 kg/ha for treatments SS, SM and MM, respectively. Catla, grass carp and carpio showed better growth and production performance in presence of mola at a higher density, while rohu, Thai punti and mrigal showed better performance when stocking density of mola was relatively low. Mola yield was almost two times higher (184 kg/ha) in absence of silver carp (MM) than (62 kg/ha) in presence of silver carp (SM). The result showed that there was a significantly (p<0.01) lower total fish production in treatment MM. But there were no significant difference in total production between treatment SS and SM.

Enhancement of fish production in a reservoir after partitioning by dikes through community participation

A reservoir of 70 acres was portioned by dikes into four manageable big ponds to get more production of fishes at Basurhat, Noakhali, Bangladesh under the supervision of local community through a society of 40 people ownership. Pangus (Pangasius hypophthalmus) @ 20,000/acre, and then fry and fingerlings of different types of fishes such as catla (Catla catla), rohu (Labeo rohita), mrigal (Cirrhina mrigala), grass carp (Ctenophmyngodon idella), bighead (Aristichthys nobili), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus cmpio) and rajpunti (Puntius gonionatus) @ 500/acre were stocked. Feed containing 25% protein was used two times daily and feed was adjusted fortnightly. After 8 months, all the fishes were weighed 0.80-2.10 kg except rajpunti (150-200 g) and tilapia (150-220 g), and a total of 25 ton of fish was harvested which was five times higher than the previous production under signal ownership. The production of fishes were increased after partitioning the lake with dikes due to proper management and control.

Studies on the growth and production of six major and exotic carps in Nasti baor, Jhenaidah, Bangladesh

An investigation on growth, production and fishery of three Indian major carps: rohu, Labeo rohita, catla, Catla catla and mrigal, Cirrhinus mrigala and three exotic carps: silver carp, Hypophthalmichthys molitrix, grass carp, Ctenopharyngodon idella, and common carp, Cyprinus carpio was carried out in Nasti baor during February to April months. In catch per unit effort (CPUE) study the highest catch/day/person (3.13 kg) and catch/day/gear (40.65 kg) was recorded in the month of March for kochal fishing. In komar fishing catch/day/person (15.08 kg) and catch/day/gear (1206 kg) was also found higher in March. Komar fishing was done only in March and April and its CPUE was greater in both the months than that of kochal. The average recovery rate (combination of all six species) was 37.80 considering the stocking from July month of the previous year. The recovery rate of common carp (54.1) was the highest and lowest (13.90) in case of silver carp. When the recovery was calculated on the basis of one year data and stocking, it was 55.6%. Analysis of production model revealed that the present production (54,806 kg/year) is less than both theoretical production (model I- 85,285 kg/year and model II -75,952 kg/year) estimated. Therefore, it may be concluded that the fish production from Nasti baor could still be increased from the present level of production.

What you should know about carp: its origin, varieties, physical appearance, feeding habits

The article discusses the different varieties of carp, their origin, physical appearance and feeding habits. The species discussed are grass carp (Ctenopharyngodon idella), silver carp (Hypophthalmichthys molitrix), bighead carp (Aristichthys nobilis), catla (Catla catla), rohu (Labeo rohita), mrigal (Cirrhinus mrigala), and common carp (Cyprinus carpio).

Diet and feeding behavior of Rhinopithecus bieti at Xiaochangdu, Tibet: Adaptations to a marginal environment

The diet and feeding ecology of a wild subpopulation of black-and-white snub-nosed monkeys (Rhinopithecus bieti) were studied at Xiaochangdu in Honglaxueshan Nature Reserve, Tibet. This region is climatologically harsher than any other inhabited by non-human primates. Black-and-white snub-nosed monkeys fed on 48 parts of 25 plant species, at least three species of lichens and seven species of invertebrates. The number of food items exploited varied markedly among seasons, with dietary diversity being greatest in spring and summer. In winter, black-and-white snub-nosed monkeys had to subsist on fallback foods such as dried grass and bark. Ubiquitous lichens formed a major dietary constituent throughout the year, contributing about 75% of feeding records. Even though lichens act as a staple, our findings signify that the monkeys at Xiaochangdu prefer feeding on foliage, which is higher in protein content than the former. We provide evidence that black-and-white snub-nosed monkeys are able to cope with an array of food items other than lichens and hence can be regarded as feeding generalists. We discuss the results with reference to previous studies on other subpopulations living in habitats that are floristically more diverse and offer more plant food items than the marginal habitat at Xiaochangdu.

牙鲆一株弹状病毒病原的分离与鉴定

从患病牙鲆中分离鉴定了一株弹状病毒(Paralichthys olivaceus rhabdovirus,PoRV)。用过滤除菌后的患病牙鲆组织匀浆液,接种不同的鱼类细胞,其中有7种鱼类细胞出现明显的病变在对病毒进行挑斑分离后,测定了PoRV的滴度,显示PoRV在敏感鱼类细胞(Grass Carp Ovary,GCO)中的滴度达到106.5TCID50/mL;绘制了PoRV生长曲线;经蔗糖密度梯度离心提纯PoRV,负染及宿主细胞超薄切片的电镜观察,显示PoRV大小约为60nm×200nm。测定了PoRV的

两种鳜病毒的共感染现象及引起感染细胞的超微变化

借助细胞培养和电镜技术,揭示了鳜球形病毒(Siniperca chuatsi spherical virus,SCSV)与鳜弹状病毒(Siniperca chuatsi rhabdovirus,SCRV)在草鱼鳍细胞(Grass carp fins,GCF)中共感染的现象。在筛选到敏感鱼类细胞系和建立了 鳜病毒体外增殖系统的基础上,取息典型病毒感染出血症的鳜组织,制备组织悬液,接种到GCF细胞中传代培养, 在攻毒后间隔不同时间收集细胞,对攻毒细胞的超薄切片进行电镜观察。揭示两种形态的鳜病毒可在同一个GCF

两株水生呼肠孤病毒部分特性的比较

水生呼肠孤病毒为感染水生动物的一类病原体,隶属于呼肠孤病毒科新建水生呼肠孤病毒属。草鱼呼肠孤病毒(Grass carp reovirus,GCRV)是引起中国南方淡水养殖草鱼暴发性出血病病原,鲅鱼呼肠孤病毒(Threadfin reovirus,TFV)是引起海水养殖鲅鱼病毒病病原。本研究将GCRV与新加坡TFV分离株进行了部分特性比较研究。结果表明,GCRV与TFV均能感染CIK细胞,但对其它鱼类细胞系的敏感性有所差异。此外,凝胶电泳与逆转录聚合酶链式扩增显示,GCRV与TFV核酸属不同的基因型。在多肽

胭脂鱼弹状病毒包涵体在培养细胞中的形成

从患致死性出血综合征的胭脂鱼 ( Myxocyprinusasiaticus Bleeker)分离到一种能产生包涵体的弹状病毒 ,称为胭脂鱼弹状病毒 ( Chinese sucker rhabdovirus,CSRV)。选择草鱼卵巢细胞系 ( Grass carp ovaries,CO)为宿主细胞 ,在接种 CSRV 3、6、9、1 2、1 8h后 ,分别取样、固定、制片、染色 ,用光学显微镜和电子显微镜观察。光镜观察结果显示 ,CSRV包涵体为直径 1～ 1 0μm的球形胞质包涵体 ;在宿主细胞中有多个

Consensus optimization on manifolds

The present paper considers distributed consensus algorithms that involve N agents evolving on a connected compact homogeneous manifold. The agents track no external reference and communicate their relative state according to a communication graph. The consensus problem is formulated in terms of the extrema of a cost function. This leads to efficient gradient algorithms to synchronize (i.e., maximizing the consensus) or balance (i.e., minimizing the consensus) the agents; a convenient adaptation of the gradient algorithms is used when the communication graph is directed and time-varying. The cost function is linked to a specific centroid definition on manifolds, introduced here as the induced arithmetic mean, that is easily computable in closed form and may be of independent interest for a number of manifolds. The special orthogonal group SO (n) and the Grassmann manifold Grass (p, n) are treated as original examples. A link is also drawn with the many existing results on the circle. © 2009 Society for Industrial and Applied Mathematics.

草鱼呼肠孤病毒感染鳍条细胞株出现的变化

<正> 草鱼出血病(Hemorrhage of grass carp)是草鱼种的一种严重疾病,通常在水温25—30％时发病,1980年水生生物研究所病毒组从草鱼肾组织超薄切片(在电镜下)观察到品格状排列的病毒颗粒,并暂名为疱疹病毒。经进一步研究,1982年正式定名为草鱼呼肠孤病毒(Reovirus of grass carp)。此病毒属双股RNA类型。把病毒接种到草鱼鳍条细胞株,在28℃、72小时以后能清晰的看到细胞病变(CPE)。病变初期,细胞受刺激后无限制地加速生长,致使细胞间隔不清,出现一些颗粒状物

草鱼出血病病毒形态结构及其理化特性的研究

<正> 草鱼出血病(Hemorrhage of grass carp)是草鱼种饲养阶段危害最严重的疾病。我所鱼病室病毒组于1978年报导了其病原研究,认为是由一种病毒所引起。1980年又报道了病原的电镜观察,在人工感染致病的草鱼肾组织的超薄切片中看到病毒颗粒,并暂名为草鱼疱疹病毒(Herpesvirus of grass carp)。为了进一步了解该病毒的特性及形态结构,近年来,我们提纯了病毒,作了一些理化特性测定和电镜观察,现将结果简报如下。

Expression regulation and functional characterization of a novel interferon inducible gene Gig2 and its promoter

Grass carp hemorrhagic virus (GCHV)-induced gene 2 (Gig2) is a novel gene previously identified from UV-inactivated GCHV-treated Carassius auratus blastulae embryonic (CAB) cells, suggesting that it should play a pivotal role in the interferon (IFN) antiviral response. In this study, a polyclonal anti-Gig2 antiserum was generated and used to study the inductive expression pattern by Western blot analysis, showing no basal expression in normal CAB cells but a significant up-regulation upon UV-inactivated GCHV, polyinosinic:polycytidylic acid (Poly I:Q and recombinant IFN (rIFN). However, constitutive expression of Gig2 is observed in all tested tissues from grass carp (Ctenopharyngodon idellus), and Poly I:C injection increases the relative amount of Gig2 protein in skin, spleen, trunk kidney, gill, hindgut and thymus. Moreover, the genomic sequence covering the whole Gig2 ORF and the upstream promoter region were amplified by genomic walking. Significantly, the Gig2 promoter contains three IFN-stimulated response elements (ISREs), nine GAAA/TfTC motifs and five gamma-IFN activating sites (GAS), which are the characteristics of genes responsive to both type I IFN and type 11 IFN. Subsequently, the complete Gig2 promoter sequence was cloned into pGL3-Basic vector, and its activity was measured by luciferase assays in the transfected CAB cells. The Gig2 promoter-driven construct is highly induced in CAB cells after treatment with Poly I:C or rIFN, and the functional capability is dependent on IFN regulatory factor 7 (IRF7), because its activity can be stimulated by IRF7. Collectively, the data provide strong evidence that Gig2 is indeed a novel IFN inducible gene and its expression is likely dependent on IRF7 upon Poly I:C or IFN. (C) 2009 Elsevier Ltd. All rights reserved.

Subcellular localization and inductive expression of the dsRNA-dependent protein kinase PKR from Japanese flounder, Paralichthys olivaceus

The double-stranded RNA (dsRNA)-dependent protein kinase (PKR) belongs to the eIF2 alpha kinase family and plays a critical role in interferon (IFN)-mediated antiviral response. Recently, in Japanese flounder (Paralichthys olivaceus), a PKR gene has been identified. In this study, we showed that PoPKR localized to the cytoplasm, and the dsRNA-binding motifs (dsRBMs) played a determinative role in protein localization. In cultured FEC cells, PoPKR was detected at a low level of constitutive expression but was highly induced after treatment with UV-inactivated grass carp hemorrhagic virus, active SMRV and Poly I:C although with different expression kinetics. In flounder, PoPKR was ubiquitously distributed in all tested tissues, and SMRV infection resulted in significant upregulation at mRNA and protein levels. In order to reveal the role of PoPKR in host antiviral response, its expression upon exposure to various inducers was characterized and further compared with that of PoHRI, which is another eIF2 alpha kinase of flounder. Interestingly, expression comparison revealed that all inducers stimulated upregulation of PoHRI in cultured flounder embryonic cells and fish, with a similar kinetics to PoPKR but to a less extent. These results suggest that, during antiviral immune response, both flounder eIF2 alpha kinases might play similar roles and that PoPKR is the predominant kinase. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.