Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

梭形纽带属在中国新纪录及矢梭形纽带绦虫再描述(绦虫纲,鲤蠢目)(英文)

报道了中国鲤蠢目纽带科绦虫1新纪录属和1新纪录种,即梭形纽带属Atractolytocestus Anthony,1958及该属矢梭形纽带绦虫A.sagittaus(Kulakovskaya et Akhmerov,1965)。梭形纽带绦虫与该科中国已记录的纽带属和许氏属绦虫的区别分别在于其卵巢后有卵黄腺存在;卵黄腺在子宫和卵巢侧面连续大量分布,睾丸向后延伸到子宫两侧,头节球状或圆锥状。细颈许氏绦虫Khawia tenuicollis Li,1964的分类学地位在该报道中被重新讨论。

草鱼呼肠孤病毒上调稀有鮈鲫鳃中TLR3和Mx基因的表达(英文)

鳃暴露在水环境中,增加了对疾病的易感性。为了研究稀有鮈鲫人工感染草鱼呼肠孤病毒过程中鳃部先天性免疫反应机制,我们克隆了抗病毒效应分子Mx基因的部分序列,用适时荧光定量PCR检测双链RNA的模式识别受体(Toll-like receptor3,TLR3)及I型干扰素指示基因Mx的表达。TLR3和Mx基因的表达在注射病毒后12h显著升高(p<0.05),TLR3的表达水平在注射后48h恢复到正常水平(p>0.05),而Mx的高水平表达一直持续到实验结束(p<0.05)。结果表明在GCRV感染中,鳃能发生局部免

马口鱼和宽鳍(鱼巤)鳃上发现寄生桡足类一新种(杯口水蚤目,鳋科)(英文)

在湖北省丹江口水库的马口鱼和宽鳍(鱼巤)的鳃上发现的寄生桡足类1新种丹江鳋。形态观察的结果表明,丹江鳋与鳋属的其他种类有很多共同特征,尤其是与博氏鳋和膨大鳋。与其它所有鳋属种类不同的是丹江鳋的第2触肢内缘光滑无刺,及其楔形第2节的外缘呈明显的弧状。以核糖体内转录间隔区(ITS)为标记进行系统进化分析,结果表明,与膨大鳋相比,博氏鳋与丹江鳋的亲缘关系更近些。无论是形态还是系统进化分析的结果都支持丹江鳋为鳋属1个独立的新种。

神农架地区珍稀植物沿河岸带的分布格局(英文)

在神农架香溪河流域内不同海拔高度沿河岸带共设置42个与河岸方向相同的10 m宽、100 m长样带进行植被调查,发现河岸带分布有珍稀保护植物14种,占神农架地区珍稀植物总数的42.4%,这些珍稀植物主要分布在1200～1800 m山地常绿阔叶林、落叶阔叶混交林带,表明在神农架地区植物群落的物种多样性在中等海拔高度上最大。TWINSPAN分类可把14种珍稀物种可划分为低海拔、中等海拔和较高海拔种组3组,DCA排序也使14种珍稀物种在反映海拔梯度的第一轴可以得到很好的展示。本文还对河岸带珍稀植物分布格局的成因进

三峡地区河岸带植物群落的特征及其分类与排序研究(英文)

本文以长江三峡干流河岸植物群落为研究对象,对群落的物种组成、物种多样性进行了分析,并利用TWINSPAN和DCA对植物群落进行等级式划分。结果表明:河岸植物区系组成较为复杂,以温带成分为主,有着较高比率的世界分布成分。灌、草丛群落之间的物种多样性差异不显著,但部分草丛的不同层次间存在较大差异。TWINSPAN 和DCA分析显示,河岸植物群落呈现沿湿度梯度方向的分布格局。图2表3参8。

Coagulation removal of melanoidins from biologically treated molasses wastewater using ferric chloride

The pigments (melanoidins) in molasses wastewater are refractory to conventional biological treatment. Ferric chloride was used as coagulant to remove color and chemical oxygen demand (COD) from molasses effluent. Using jar test procedure, main operating conditions such as pH and coagulant dosage were investigated. Under the optimum conditions, up to 86% and 96% of COD and color removal efficiencies were achieved. Residual turbidity in supernatant was less than 5 NTU and Fe3+ concentration was negligible because of effective destabilization and subsequent sedimentation. The results of high performance size exclusion chromatography (HPSEC) show that low molecular weight (MW) fraction of melanoidins is more reactive than high MW fraction and increase in the concentration of the lowest MW organic group is related to the capacity of charge neutralization. Aggregate size measurement reveals the size effect on the settleability of flocs formed, with larger flocs settling more rapidly. Charge neutralization and co-precipitation are proposed as predominant coagulation mechanism under the optimum conditions. (C) 2009 Elsevier B.V. All rights reserved.

KHAWIA SAUROGOBII N. SP (CESTODA: CARYOPHYLLIDEA) FROM FRESHWATER FISH SAUROGOBIO SPP. (CYPRINIDAE) IN CHINA

Khawia saurogobii n. sp. is described from the intestine of the cyprinid fishes Saurogobio dabryi and Saurogobio dumerili in China. The new species belongs to the Lytocestidae and is placed in Khawia because of its afossate scolex, vitelline follicles in the cortical parenchyma, uterus not looping anterior to the cirrus sac, gonopores separate but close together in distinct genital atrium, external seminal vesicle absent, and postovarian follicles present. The new species differs from other congeneric species by the shape of the body markedly tapering posteriorly from the end of the anterior third, the shape of the scolex that is very short and markedly wider than the neck, spatulate without incisions, but shallow superficial grooves, vitelline follicles and testes starting immediately posterior to the scolex, and an ovary with long, posterior arms bent medially, thus giving the shape of an inverted A.

Fridericia liangi sp nov (Enchytraeidae, Oligochaeta) from Changbaishan Mountain, China

We describe one new enchytraeid species, Fridericia liangi sp. nov., from Mt. Changbaishan, Jilin Province, northeastern China. It was collected from soils at the foot of Changbaishan Mountain and is distinguished from all known congeners by the following combination of characters: 1) no lateral chaetae, only ventral chaetae throughout, 2) a maximum of four chaetae in ventral preclitellar bundles, 3) one chaeta in ventral postclitellar bundles, 4) dorsal pores from VII on, 5) esophageal appendages unbranched, 6) coelomocytes without refractile vesicles, 7) clitellum girdle shaped, well developed, 8) no subneural glands, and 9) spermathecae simple.

Temporal Coherence of Chlorophyll a during a Spring Phytoplankton Bloom in Xiangxi Bay of Three-Gorges Reservoir, China

Algal bloom phenomenon was defined as "the rapid growth of one or more phytoplankton species which leads to a rapid increase in the biomass of phytoplankton", yet most estimates of temporal coherence are based on yearly or monthly sampling frequencies and little is known of how synchrony varies among phytoplankton or of the causes of temporal coherence during spring algal bloom. In this study, data of chlorophyll a and related environmental parameters were weekly gathered at 15 sampling sites in Xiangxi Bay of Three-Gorges Reservoir (TGR, China) to evaluate patterns of temporal coherence for phytoplankton during spring bloom and test if spatial heterogeneity of nutrient and inorganic suspended particles within a single ecosystem influences synchrony of spring phytoplankton dynamics. There is a clear spatial and temporal variation in chlorophyll a across Xiangxi Bay. The degree of temporal coherence for chlorophyll a between pairs of sites located in Xiangxi Bay ranged from -0.367 to 0.952 with mean and median values of 0.349 and 0.321, respectively. Low levels of temporal coherence were often detected among the three stretches of the bay (Down reach, middle reach and upper reach), while high levels of temporal coherence were often found within the same reach of the bay. The relative difference of DIN between pair sites was the strong predictor of temporal coherence for chlorophyll a in down and middle reach of the bay, while the relative difference in Anorganic Suspended Solids was the important factor regulating temporal coherence in middle and upper reach. Contrary to many studies, these results illustrate that, in a small geographic area (a single reservoir bay of approximately 25 km), spatial heterogeneity influence synchrony of phytoplankton dynamics during spring bloom and local processes may override the effects of regional processes or dispersal.

Ontogeny of IgM-producing cells in the mandarin fish Siniperca chuatsi identified by in situ hybridisation

The ontogeny of IgM-producing cells was studied in juvenile mandarin fish Simperca chuatsi, an important fish in China's aquaculture sector. The IgM-producing cells were localised through in situ hybridisation with a probe complementary to the Ig mu-chain in lymphoid-related tissues, including head kidney, spleen, thymus, intestine and gills. In head kidney, transcripts of Ig mu were first detected at 20 days post-hatching (dph) with a few positive signals. and the number of IgM-producing cells increased obviously from 39 dph onwards. At 136 dph, a large amount of positive cells were observed in the entire organ with clusters of these cells located around the blood vessels. In spleen, IgM-producing cells were found from 26 dph onwards, followed by an increase until 67 dph: clusters of positive cells were also detected around blood vessels at 102 dph. In thymus, IgM-producing cells were first observed at 39 dph; thereafter, no obvious increase was detected until 78 dph. The positive cells in thymus were distributed mainly in the outer zone of thymus. A few IgM-producing cells were still observed in thymus of 1-year-old mandarin fish. IgM-producing cells were not detected in the intestine until 87 dph, with several discrete positively stained cells distributed in the lamina propria. IgM-producing cells, scattered mainly in primary gill filaments around blood vessels, were detected in gills from 90 dph. As in other teleosts, these results indicated that the head kidney appears to be the primary organ for IgM production in mandarin fish, and IgM-producing cells exist in all organs examined in the present study, implying their lymphoid role in fish. In addition, it is suggested that vaccination after 20 dph may be much more effective in mandarin fish. (C) 2009 Elsevier B.V. All rights reserved.

Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau

National Natural Science Foundation of China (NSFC) [30225008, 30300036, 30530120]; Key Innovation Plan [KSCX2-SW-106]; National Basic Research Project in China [2005cb422005]; National Natural Science Foundation of China [30600062]

Physiological responses to capture and handling of free-ranging male Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis)

We captured free-ranging male Yangtze finless porpoises over three seasons and assayed leukocytes and serum biochemistry to investigate physiological responses to the capture and handlings. Serum thyroid hormones (THs) declined sharply in those porpoises compared with hormone variation in a captive male finless porpoise. Hypernatremia and hypokalemia were also significant in the free-ranging animals suggesting that conservation of serum sodium might be acutely vital for this freshwater subspecies. The animals captured in spring showed more significant neutrophilia and eosinopenia than those captured in autumn suggesting that they may be more affected by capture during the breeding season. Furthermore, physical examination of porpoises when out of the water was apparently stressful, particularly when they were kept out of the water for longer periods. However, an increase in circulating THs may be an adaptive response to accommodate these short-term stresses.

Mechanism study on the frequent variations of cell-bound microcystins in cyanobacterial blooms in Lake Taihu: Implications for water quality monitoring and assessments

Although Microcystis-based toxins have been intensively studied, previous studies using laboratory cultures of Microcystis strains are difficult to explain the phenomenon that microcystin concentrations and toxin variants in natural blooms differ widely and frequently within a short-term period. The present study was designed to unravel the mechanisms for the frequent variations of intracellular toxins related to the differences in cyanobacterial colonies during bloom seasons in Lake Taihu, China. Monitoring of Microcystis colonies during warm seasons indicated that the variations in microcystins in both concentrations and toxin species were associated with the frequent alteration of Microcystis colonies in Lake Taihu. High concentration of microcystins in the blooms was always associated with two Microcystis colonies, Microcystis flos-aquae and Microcystis aeruginosa, whereas when Microcystis wesenbergii was the dominant colonial type, the toxin production of the blooms was low. Additionally, environmental factors such as temperature and nutrition were also shown to have an effect on the toxin production of the blooms, and may also potentially influence the Microcystis species present. The results of the present study provides insight into a new consideration for quick water quality monitoring, assessment and risk alert in cyanobacterium- and toxin-contaminated freshwaters, which will be beneficial not only for water agencies but also for public health. (C) 2009 Elsevier Ltd. All rights reserved.

Evolutionary Conservation of Dazl Genomic Organization and its Continuous and Dynamic Distribution Throughout Germline Development in Gynogenetic Gibel Carp

To investigate germline development and germ cell specification, we identified a Dazl homolog (CagDazl) from gynogenetic gibel carp (Carassius auratus gibelio). Its cDNA sequence and BAC clone sequence analyses revealed the genomic organization conservation and conserved synteny of the Dazl family members and their neighborhood genes among vertebrates, especially in fish. Moreover, a polyclonal antibody specific to CagDazl was produced and used to examine its expression and distribution throughout germline development at protein level. Firstly, ovary-specific expression pattern of CagDazl was confirmed in adult tissues by RT-PCR and Western blot. In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. Furthermore, the CagDazl is abundant and continuous throughout germline development and germ cell specification including primordial germ cell (PGC) formation, oogonium differentiation, oocyte development, and embryogenesis, and the dynamic distribution occurs at different development stages. The data suggest that maternal CagDazl might play an important role in gibel carp PGC formation. Therefore, CagDazl is a useful and specific marker for tracing germ plasm and germ cell development in the gynogenetic gibel carp. In addition, in comparison with previous studies in sexual reproduction species, the continuous and dynamic distribution of CagDazl protein in the germ plasm throughout the life cycle seems to have significant implication in sex evolution of vertebrates. J. Exp. Zool. (Mol. Deu. Euol.) 312B:855-871, 2009. (C) 2009 Wiley-Liss, Inc.