Group Size and Composition of Black．and．White Snub．nosedMonkey(rhinopithecus)Estimated by Faecesof Sleeping Sites at Baima Snow Mountain

介绍了应用过夜地粪便来估计白马雪山黑白仰鼻猴群大小和组成的一种方法。该物种以单雄多雌单 元和全雄组的形式在树上过夜。粪粒根据其大小可分为3种类型：成年雄性的(最大)、成年雌性的(中等大小)和 未成年个体的(最小)。2000一2001年，搜集了滇西北白马雪山国家级自然保护区北部南任村(99。04 7E，28。34 7N) 附近黑白仰鼻猴群每个季节2个过夜地的粪粒。根据2001年11月猴群通过开阔地的数据来确定猴群组成。每个 季节，由于单雄多雌单元的成年个体数与其粪粒数正相关，所以二者回归直线的斜率可以看作是每个个体每晚 的平均排便量。由于该物种的栖息地主要为高山峡谷，而且能见度较低，因此，利用过夜地粪便比以前通过猴群 活动痕迹来估计猴群大小和组成相对准确、可靠。从估计成年雌性个体数的角度看，利用粪粒来估计种群大约有 9．4％的偏差。导致偏差的可能原因有杂草和灌丛对粪粒准确计数的影响、个体排粪率的差异以及成年雄性最小 粪粒与成年雌性最大粪粒的混淆等。该方法适应于栖息地和主要食物与本文研究种群相似的其他种群。

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Sleeping sites of Rhinopithecus bieti at Mt. Fuhe, Yunnan

Data on sleeping site selection were collected for a group of black-and-white snub-nosed monkeys (Rhinopithecus bieti; around 80) at Mt. Fuhe, Yunnan, China (99degrees20'E, 26degrees25'N, about 3,000 m asl) from November 2000 to January 2002. At the site mainly three vegetation types were present in an elevation-ascending order: deciduous broad leaf forest, mixed coniferous and broad leaf forest, and dark coniferous forest. In addition, bamboo forest presented in areas burned in 1958. Sleeping sites (n = 10) were located in the coniferous forest, where trees were the tallest, bottommost branches were the highest, the diameter of crowns was the second largest, and the gradient of the ground was the steepest. Monkeys usually kept quiet during entering and staying at a sleeping site. The site choice and the quietness may be tactics to avoid potential predators. In the coniferous forest, however, monkeys did not sleep in the valley bottom where trees were the largest, but frequently slept in the middle of the slope towards the east/southeast, in the shadow of ridges in three other directions, to avoid strong wind and to access sunshine; in winter-spring, they ranged in a more southern and lower area than in summer-autumn. These may be behavioral strategies to minimize energy stress in the cold habitat. Monkeys often slept in the same sleeping site on consecutive nights, which reflected a reduced pressure of predation probably due to either the effectiveness of anti-predation through sleeping site selection, or the population decline of predators with increasing human activities in the habitat. The group's behavioral responses to interactive and sometimes conflicting traits of the habitat are site-specific and conform to expectations for a temperate zone primate.

Sleeping sites of black-and-white snub-nosed monkeys (Rhinopithecus bieti) at Baima Snow Mountain, China

Data on sleeping sites of a group of black-and-white snub-nosed monkeys Rhinopithecus bieti (Colobinae, Primates) were collected between April-July and September-December 2001 to try to determine the factors affecting site selection at Nanren (99 degrees

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.

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.

Expression pattern, cellular localization and promoter activity analysis of ovarian aromatase (Cyp19a1a) in protogynous hermaphrodite red-spotted grouper

Aromatase plays a key role in sex differentiation of gonads. In this study, we cloned the full-length cDNA of ovarian aromatase from protogynous hermaphrodite red-spotted grouper (Epinephelus akaara), and prepared the corresponding anti-EaCyp19a1a antiserum. Western blot and immunofluorescence studies revealed ovary-specific expression pattern of EaCyp19a1a in adults and its dynamic expression change during artificial sex reversal. EaCyp19a1a was expressed by follicular cells of follicular layer around oocytes because strong EaCyp19a1a immunofluorescence was observed in the cells of ovaries. During artificial sex reversal, EaCyp19a1a expression dropped significantly from female to male, and almost no any positive EaCyp19a1a signal was observed in testicular tissues. Then, we cloned and sequenced a total of 1967 bp T-flanking sequence of EaCyp19a1a promoter, and showed a number of potential binding sites for some transcriptional factors, such as SOX5, GATA gene family, CREB, AP1, FOXL1, C/EBP, ARE and SF-1. Moreover, we prepared a series of 5' deletion promoter constructs and performed in vitro luciferase assays of EaCyp19a1a promoter activities. The data indicated that the CREB regulation region from -1010 to -898 might be a major cis-acting element to EaCyp19a1a promoter, whereas the elements GATA and SOX5 in the region from -1216 to -1010 might be suppression elements. Significantly, we found a common conserved sequence region in the fish ovary-type aromatase promoters with identities from 93% to 34%. And, the motifs of TATA box, SF-1, SOX5, and CREB existed in the region and were conserved among the most of fish species. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

Changes in benthic algal communities following construction of a run-of-river dam

Ecological responses to dam construction are poorly understood, especially for downstream benthic algal communities. We examined the responses of benthic algal communities in downstream reaches of a tributary of the Xiangxi River, China, to the construction of a small run-of-river dam. From February 2003 to August 2006, benthic algae, chemical factors, and habitat characteristics were monitored upstream and downstream of the dam site. This period spanned 6 mo before dam construction and 37 mo after dam construction. Benthic algal sampling yielded 199 taxa in 59 genera that belonged to Bacillariophyta, Chlorophyta, and Cyanophyta. Some physical factors (flow velocity, water depth, and channel width) and 3 algal metrics (diatom species richness, Margalef diversity, and % erect individuals) were significantly affected by the dam construction, whereas chemical factors (e.g., NH4-N, total N, SiO2) were not. Nonmetric multidimensional scaling (NMS) ordinations showed that overall algal assemblage structure downstream of the dam sites was similar to that of upstream control sites before dam construction and for 1 year after dam construction (p > 0.05). However, sites belonging to upstream and downstream reaches were well separated on NMS axis 1 during the 2(nd) and 3(rd) years after dam construction. Our results suggest that impacts of dam construction on benthic algal communities took 2 to 3 y to emerge. Further development of a complete set of indicators is needed to address the impact of small-dam construction. Our observations underscore the need for additional studies that quantify ecological responses to dam construction over longer time spans.

Spatial distribution of benthic algae in the Gangqu River, Shangrila, China

This study consisted of sampling benthic algae at 32 sites in the Gangqu River, an important upstream tributary of the Yangtze River. Our aims were to characterize the benthic algae communities and relationships with environmental variables. Among the 162 taxa observed, Achnanthes linearis and Achnanthes lanceolata var. elliptica were the dominant species (17.10% and 14.30% of the total relative abundance, respectively). Major gradients and principal patterns of variation within the environmental variables were detected by principal component analysis (PCA). Then non-metric multidimensional scaling (NMS) divided all the sites into three groups, which were validated by multi-response permutation procedures (MRPP). Canonical correspondence analysis (CCA) indicated that three environmental variables (TN, TDS, and TP) significantly affected the distribution of benthic algae. Weighted averaging regression and cross-calibration produced strong models for predicting TN and TDS concentration, which enabled selection of algae taxa as potentially sensitive indicators of certain TN and TDS levels: for TN, Achnanthes lanceolata, Achnanthes lanceolata var. elliptica, and Cymbella ventricosa var. semicircularis; for TDS, Cocconeis placentula, Cymbella alpina var. minuta, and Fragilaria virescens. The present study represents an early step in establishing baseline conditions. Further monitoring is suggested to gain a better understanding of this region.

Expressional induction of Paralichthys olivaceus cathepsin B gene in response to virus, poly I:C and lipopolysaccharide

Cathepsin B is a lysosomal cysteine protease of the papain-like enzyme family with multiple biological functions. In this study, Paralichthys olivaceus cathepsin B (PoCatB) cDNA was isolated from flounder embryonic cells (FEC) treated with UV-inactivated grass carp hemorrhage virus (GCHV) and subsequently identified as a vitally induced gene. The full length cDNA of PoCatB is 1801 bp encoding 330-amino acids. The deduced protein has high homology to all known cathepsin B proteins, containing an N-terminal signal peptide, cysteine protease active sites, the occluding loop segment and a glycosylation site, all of which are conserved in the cathepsin B family. PoCatB transcription of FEC cells could be induced by turbot (Scophthalmus maximus) rhabdovirus (SMRV), UV-inactivated SMRV, UV-inactivated GCHV, poly I:C or lipopolysaccharide (LPS), and SMRV or poly I:C was revealed to be most effective among the five inducers. In normal flounder, PoCatB mRNA was detectable in all examined tissues. Moreover, SMRV infection could result in significant upregulation of PoCatB mRNA, predominantly in spleen, head kidney, posterior kidney, intestine, gill and muscle with 18.2,10.9, 24.7,12, 31.5 and 18 fold increases at 72 h post-infection respectively. These results provided the first evidence for the transcriptional induction of cathepsin B in fish by virus and LPS, indicating existence of a novel function in viral defense. (C) 2008 Elsevier Ltd. All rights reserved.

Phylogenetic relationships of Cyprinidae (Teleostei : Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1

The family Cyprinidae is widely distributed in East Asia, and has the important phylogenetic significance in the fish evolution. In this study, the 5' end partial sequences (containing exon 1, exon 2 and indel 1) of S6K1 gene were obtained from 30 representative species in Cyprinidae and outgroup using PCR amplification and sequencing. The phylogenetic relationships of Cyprinidae were reconstructed with neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian methods. Myxocyprinus asiaticus (Catostomidae) was assigned to the outgroup taxon. Similar phylogenetic relationships within the family Cyprinidae were achieved with the four analyses. Leuciscini and Barbini were monophyletic lineages respectively with the high nodal supports. Leuciscini comprises Hypophthalmichthyinae, Xenocyprinae, Cultrinae, Gobioninae, Acheilognathinae and East Asian species of Leuciscinae and Danioninae. Monophyly of East Asian clade was supported with high nodal support. Barbini comprises Schizothoracinae, Barbinae, Cyprininae and Labeoninae. The monophyletic lineage consisting of Danio rerio, D. myersi, and Rasbora trilineata was basal in the tree. In addition, the large fragment indels in intron 1 were analyzed to improve the understanding of Cyprinidae relationships. The results showed that the large fragment indels were correlated with the relations among species. Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size.

Site-directed gene integration in transgenic zebrafish mediated by cre recombinase using a combination of mutant Lox sites

With current gene-transfer techniques in fish, insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences, and multiple gene interactions make gene expression experiments difficult to interpret and fish phenotype less predictable. To meet different fish engineering needs, we describe here a gene targeting model in zebrafish. At first, four target zebrafish lines, each harboring a single genomic lox71 target site, were generated by zebrafish transgenesis. The zygotes of transgenic zebrafish lines were coinjected with capped Cre mRNA and a knockin vector pZklox66RFP. Site-specific integration event happened from one target zebrafish line. In this line two integrant zebrafish were obtained from more than 80,000 targeted embryos (integrating efficiency about 10(-4) to 10(-5)) and confirmed to have a sole copy of the integrating DNA at the target genome site. Genomic polymerase chain reaction analysis and DNA sequencing verified the correct gene target events where lox71 and lox66 have accurately recombined into double mutant lox72 and wild-type loxP. Each integrant zebrafish chosen for analysis harbored the transgene rfp at the designated egfp concatenates. Although the Cre-mediated recombination is site specific, it is dependent on a randomly placed target site. That is, a genomic target cannot be preselected for integration based solely on its sequence. Conclusively, an rfp reporter gene was successfully inserted into the egfp target locus of zebrafish genome by Cre-lox-mediated recombination. This site-directed knockin system using the lox71/lox66 combination should be a promising gene-targeting platform serving various purposes in fish genetic engineering.