Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

Phomoeuphorbins A-D, azaphilones from the fungus Phomopsis euphorbiae

Four azaphilones, named phomoeuphorbins A-D (1-4) were isolated from cultures of Phomopsis euphorbiae, an endophytic fungus isolated from Trewia nudiflora. Structures of 1-4 were established on the basis of spectroscopic analyses, including application of

Lycojapodine A, a Novel Alkaloid from Lycopodium japonicum

Lycojapodine A, a novel C16N-type Lycopodium alkaloid with an unprecedented 6/6/6/7 tetracyclic ring system, was isolated from the club moss Lycopodium japonicum. The structure and relative stereochemistry were elucidated on the basis of spectroscopic dat

Anti-human Immunodeficiency Virus-1 Constituents of the Bark of Poncirus trifoliata

A total of 36 compounds (1-36) were obtained from the stem bark of Poncirus trifoliata including three new prenylated flavonoids, (-)-5,4'-dihydroxy-7,8-[(3 '',4 ''-cis-dihydroxy-3 '',4 ''-dihydro)-2 '',2 ''-dimethylpyrano]-flavone (1), (-)-5,4'-dihydroxy-7,8-[(3 ''-hydroxy-4 ''-one)-2 '',2 ''-dimethylpyrano]-flavone (2), and (-)-5,4'-dihydroxy-7,8-[(cis-3 ''-hydroxy-4 ''-ethoxy-3 '',4 ''-dihydro)-2 '',2 ''-dimethylpyrano]-flavone (3). The new structures were elucidated by means of spectroscopic methods. Compounds 1-20 were evaluated for their anti-human immunodeficiency virus-1 (HIV-1) activity, in which 2 showed significant anti-HIV-1 activity with high therapeutic index (T1) of 143.65.

Chemical Constituents from the Leaves and Stems of Schisandra lancifolia

A new nortriterpenoid, 20-hydroxymicrandilactone D (1) and a novel lignan glycoside, lancilignanside A (2) were isolated from leaves and stems of Schisandra lancifolia, together with three known nortriterpenoids (3-5) and nine known phenolics (6-14). The structures of new compounds 1 and 2 were determined by detailed analysis of their 1D and 2D NMR spectra, and chemical evidences. In addition, compounds 1-2, 6-7, and 9-11 showed anti-human immunodeficiency virus (HIV)-1 activities with 50% effective concentration (EC50) in the range of 3.0-99.0 mu g/ml. Compound 12 was not bioactive in this assay with EC50 more than 200 mu g/ml.

氟代柠檬酸对体外培养的神经胶质瘤细胞G422增殖的抑制效应

为研究氟代柠檬酸(Fluorocitrate)对体外培养的神经胶质瘤细胞生长的影响,采用MTT法研究不同的氟代柠檬酸浓度(0.0025mmol/L,0.005mmol/L,0.01 mmol/L,0.025mmol/L和0.1 mmol/L)和作用时间(36h,48h和60h)对神经胶质瘤细胞G422增殖的影响.结果发现:(1)氟代柠檬酸可抑制G422细胞的增殖,并且其抑制作用随氟代柠檬睃浓度的增加而增强;(2)高浓度(0.01 mmol/L,0.025 mmol/L和0.1 mmol/L)氟代柠檬酸对G422细胞的增殖抑制作用随作用时问的延长而增强:(3)低浓度(0.0025mmol/L和0.005mmol/L)氟代柠檬酸对G422细胞的增殖抑制作用不随作用时间的延长而改变.实验表明,氟代柠檬酸能够抑制神经胶质瘤细胞的增殖,其抑制能力随氟代柠檬酸浓度的增加和作用时间的延长而加强.

Delta EEG Activity in Left Orbitofrontal Cortex in Rats Related to Food Reward and Craving

眶额叶皮质与中脑边缘多巴胺奖赏系统有着复杂的相互纤维联系.先前的研究探讨了药物成瘾过程中眶额叶皮质的脑电活动.在本实验中,将探讨食物奖赏和渴求过程中该皮质的脑电活动.实验采用了两个环境:对照环境和食物刺激相关的环境.首先,训练大鼠在食物刺激相关的环境中吃巧克力花生豆,而后在该环境中设置两种不同的刺激方式:能看到和闻到但不能吃到(渴求实验),或者仍旧可以吃到巧克力花生豆(奖赏实验):同时进行左侧眶额叶皮质的脑电记录.结果发现,在食物刺激相关的环境中大鼠Delta频段(2-4Hz)的脑电活动与食物刺激显著相关,此外,与在对照环境中相比,其相对功率在食物渴求时下降而在食物奖赏时升高.本实验表明,食物相关的奖励可以改变大鼠眶额叶皮质的脑电活动,而且,Delta频段的脑电活动能够作为监测该奖励的一个指标.

Crossmodal effects of Guqin and piano music on selective attention: An event-related potential study

To compare the effects of music from different cultural environments (Guqin: Chinese music; piano: Western music) on crossmodal selective attention, behavioral and event-related potential (ERP) data in a standard two-stimulus visual oddball task were reco

Detour behavior changes associated with prenatal morphine exposure in 11-day-old chicks

The central nervous system exhibits remarkable plasticity in early life. Prenatal morphine exposure may induce adverse behavioral effects on the neonate and the developing offspring. In the present study, we investigated the effect of prenatal morphine exposure (daily from embryonic days 12-16, 20 mg/kg) on 11-day-old chicks using two forms of spatial paradigms: one trial detour behavior task in which animals must bypass an obstacle to reach the desired goal without any training and detour learning task which required several trials of training to reach the detour criterion. The results showed that, on the condition that chicks could successfully detour in the first trial, morphine exposed chicks exhibited longer detour latency to finish the task, coupled by a preference for turning right versus turning left. In contrast, no significant difference in learning and memory was found in detour learning task between morphine exposed chicks and saline chicks. These findings suggest specific behavioral changes associated with prenatal exposure to opioids during mid to late gestation, also raise attention to the possible health hazard from pregnancy drug use in everyday life. (C) 2010 ISDN. Published by Elsevier Ltd. All rights reserved.

Changes of urinary steroid conjugates and gonadotropin excretion in the menstrual cycle and pregnancy in the Yunnan snub-nosed monkey (Rhinopithecus bieti)

The Yunnan snub-nosed monkey (Rhinopithecus bieti) is one of the most endangered species in the world, and it is endemic to China. According to our knowledge, there was no information on reproduction for this species. The present study was designed to und

Vitrification of Yunnan Yellow Cattle oocytes: work in progress

The objective of this study was to provide a simple cryopreservation method for oocytes from Yunnan Yellow Cattle and facilitate preservation efforts in this native Chinese breed, which is threatened by agricultural modernization. Cumulus-oocyte complexes (COCs) were collected from slaughterhouse ovaries and matured in vitro for 22-24 h, then selected for cryopreservation. Vitrification in open pulled straws (OPS) or in microdrops on a cooled metal surface (solid surface vitrification, SSV) was compared. The OPS vitrification solution consisted of 20% ethylene glycol (EG) and 20% DMSO. The SSV solution was a mixture of 35% EG, 5% polyvinyl-pyrrolidon (PVP) and 0.4 M trehalose. Vitrified and warmed oocytes were either fertilized in vitro or parthenogenetically activated. The rates of cleavage and development to blastocysts of fertilized oocytes following OPS versus SSV were not statistically different (38.3 and 12.5% versus 35.8 and 6.0%, respectively). The corresponding rates of parthenogenetic development to blastocysts were also not different (8.2 versus 3.5%, respectively). Development to blastocysts of non-vitrified controls following fertilization was significantly higher than that of the vitrified oocytes (22.6%, P < 0.05). These results demonstrate for the first time, that although both OPS and SSV procedures reduced embryonic development, Yunnan Yellow Cattle oocytes are capable of developing to blastocysts following cryopreservation. (C) 2002 Elsevier Science Inc. All rights reserved.

Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection

In one of our recent studies, two HCV genotype 6 variants were identified in patients from Hong Kong and Guangxi in southern China, with injection drug use and HIV-1 co-infection. We report the complete genomic sequences for these two variants: GX004 and

A revision of the white-toothed shrews (Crocidura) of Southern China

Many systematic relationships among Chinese white-toothed shrews of genus Crocidura are presently unresolved. In this paper, a taxonomic revision of Crocidura from Southern China is presented. We studied 338 specimens from Burma, China, Korea, Pakistan, Turkey, Middle and Central Asia, and Russia (Appendix I), 285 of which had complete skulls that were analyzed with principal component and discriminant analyses. Results indicated that 6 species of Crocidura can be recognized in South China. C. fuliginosa occurs in Southwestern and Eastern China, C. attenuata is broadly distributed throughout Southern China, and C. horsfieldii is restricted to the southern part of China. C vorax and C. rapax, usually placed as synonyms of the European C russula, are recognized as 2 valid species whose ranges overlap in Southwestern China. C. shantungensis of Eastern Asia extends to the northern part of Southern China and is distinct from C. suaveolens and C. gmelini of Middle and Central Asia, respectively.

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene. (C) 2004 Elsevier Inc. All rights reserved.