Sequence Characterization of the MC1R Gene in Yak (Poephagus grunniens) Breeds with Different Coat Colors

Melanocortin 1 receptor (MC1R) gene plays a key role in determining coat color in several species, including the cattle. However, up to now there is no report regarding the MC1R gene and the potential association of its mutations with coat colors in yak (

Mass rearing of Aphidius gifuensis (Hymenoptera : Aphidiidae) for biological control of Myzus persicae (Homoptera : Aphididae)

The green peach aphid, Myzus persicae, is a major pest of tobacco, Nicotiana tabacum, in Yunnan province, China, where its control still depends on the use of insecticides. In recent years, the local government and farmers have sought to improve the biological control of this tobacco pest. In this paper, we present methods for mass rearing Aphidius gifuensis, a dominant endoparasitoid of M. persicae on tobacco plants in this region. The tobacco cultivar K326 (N. tabacum) was used as the host plant and M. persicae as the host insect. In the greenhouse, we collected tobacco seedlings for about 35 days (i.e., until the six-true-leaf stage), transferred them to 7.5-cm diameter pots, and kept these plants in the greenhouse for another 18 days. These pots were then transferred to an insectary-greenhouse, where the tobacco seedlings were inoculated with five to seven wingless adult M. persicae per pot. After 3 days, the infested seedlings were moved to a second greenhouse to allow the aphid population to increase, and after an additional 4 +/- 1 days when 182 +/- 4.25 aphid adults and nymphs were produced per pot, they were inoculated with A. gifuensis. With this rearing system, we were able to produce 256 +/- 8.8 aphid mummies per pot, with an emergence rate of 95.6 +/- 2.45%; 69% were females. The daily cost of parasite production (recurring costs only) was US$ 0.06 per 1000 aphid mummies. With this technique, we released 109 800 parasitoids in 1998, 196 000 in 1999, 780 000 in 2000, and 5 600 000 in 2001 during a 2-month period each year This production method is discussed with respect to countrywide usage in biological control and integrated control of M. persicae.

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)

SNPNB is a user-friendly and platform-independent application for analyzing Single Nucleotide Polymorphism NeighBoring sequence context and nucleotide bias patterns, and subsequently evaluating the effective SNP size for the bias patterns observed from the whole data. It was implemented by Java and Perl. SNPNB can efficiently handle genome-wide or chromosome-wide SNP data analysis in a PC or a workstation. It provides visualizations of the bias patterns for SNPs or each type of SNPs.

Development and use of parasitoids (Hymenoptera : Aphidiidae & Aphelinidae) for biological control of aphids in China

A review of aphid parasitoids in China with special emphasis on their production, utilization, and conservation is presented with a brief history of Chinese biological control. Twenty genera, 99 species of Aphidiidae and two genera, 11 species of Aphelinidae were recorded in China. Each parasitoid is listed with a brief description of aphids, host plants, areas of study such as taxonomy, biology, bionomics, geographic distribution, rearing, and literature citations. Achievements, status, and problems in aphid parasitoid production, utilization, conservation, and future prospects are detailed for dominant aphid parasitoids such as Aphidius gifuensis Ashmead, A. ervi Haliday and Aphelinus mali Haldeman. Finally, opportunities and challenges of commercialization commercialization of natural enemies, especially aphid parasitoids, in China, are analyzed and discussed.

Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences

A genome-wide view of sequence mutability in mice is still limited, although biologists usually assume the same scenario for mice as for humans. In this study, we examined the sequence context in the local environment of 482,528 mouse single nucleotide po

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Effects of temperature and light on the growth and geosmin production of Lyngbya kuetzingii (Cyanophyta)

The effects of temperature and light on the growth and geosmin production of Lyngbya kuetzingii were determined. Of the three temperatures tested, 10, 25 and 35A degrees C, the maximal geosmin concentration and geosmin productivity were yielded at 10A degrees C, while the highest chl a production was observed at 25A degrees C. In the studies on light intensity, the maximal geosmin concentration and geosmin productivity were observed at 10 mu mol m(-2) s(-1), while the highest chl a production was at 20 mu mol m(-2) s(-1). It was suggested that more geosmin was synthesized with lower chl a demand. Meanwhile, the relative amounts of extra- and intracellular geosmin were investigated. Under optimum growth conditions (20 mu mol m(-2) s(-1), 25A degrees C; BG-11 medium), the amounts of extracellular geosmin increased as the growth progressed and reached the maximum in the stationary phase, while the intracellular geosmin reached its maximum value in the late exponential phase, and then began to decline. However, under the low temperature (10A degrees C) or light (10 mu mol m(-2) s(-1)) conditions, more intracellular geosmin was synthesized and mainly accumulated in the cells. The proportions of extracellular geosmin were high, to 33.33 and 32.27%, respectively, during the stationary phase at 35A degrees C and 20 mu mol m(-2) s(-1). It was indicated that low temperature or light could stimulate geosmin production and favor the accumulation of geosmin in cells, while more intracellular geosmin may be released into the medium at higher temperatures or optimum light intensity.

Effects of arsenate on the growth and microcystin production of Microcystis aeruginosa isolated from Taiwan as influenced by extracellular phosphate

Arsenic pollution and eutrophication are both prominent issues in the aquaculture ponds of Taiwan. It is important to study the effects of arsenic on algal growth and toxin production in order to assess the ecological risk of arsenic pollution, or at least to understand naturally occurring ponds. The sensitivity of algae to arsenate has often been linked to the structural similarities between arsenate and phosphate. Thus, in this study we examined the effects of arsenate (10(-8) to 10(-4) M) on Microcystis aeruginosa TY-1 isolated from Taiwan, under two phosphate regimes. The present study showed that M. aeruginosa TY-1 was arsenate tolerant up to 10(-4) M, and that this tolerance was not affected by extracellular phosphate. However, it seems that extracellular phosphate contributed to microcystin production and leakage by M. aeruginosa in response to arsenate. Under normal phosphate conditions, total toxin yields after arsenate treatment followed a typical inverted U-shape hormesis, with a peak value of 2.25 +/- 0.06 mg L-1 in the presence of 10(-7) M arsenate, whereas 10(-8) to 10(-6) M arsenate increased leakage of similar to 75% microcystin. Under phosphate starvation, total toxin yields were not affected by arsenate, while 10(-6) and 10(-5) M arsenate stimulated microcystin leakage. It is suggested that arsenate may play a role in the process of microcystin biosynthesis and excretion. Given the arsenic concentrations in aquaculture ponds in Taiwan, arsenate favors survival of toxic M. aeruginosa in such ponds, and arsenate-stimulated microcystin production and leakage may have an impact on the food chain.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Cytochemical changes in the developmental process of Nostoc sphaeroides (cyanobacterium)

There are several apparent developmental stages in the life cycle of Nostoc sphaeroides Kutzing, an edible cyanobacterium found mainly in paddy fields in central China. The cytochemical changes in developmental stages such as hormogonia, aseriate stage, filamentous stage and colony in N. sphaeroides were examined using fluorescent staining and colorimetric methods. The staining of acidic and sulfated polysaccharides increased with development when hormogonia were used as the starting point. Acidic polysaccharides (AP) were most abundant at the aseriate stage and then decreased, while the sulfated polysaccharides (SP) were highest at the colony stage. Quantitatively, along the developmental process from hormogonia to colony, total carbohydrates first increased, then became stable, and then reached their highest level at the colony stage, while reducing sugars were highest at the hormogonia stage and then decreased sharply once development began. SP were not detectable in the hot water soluble polysaccharides (HWSP), and hormogonia had the lowest content of AP, while old colonies had the highest. The AP content of the aseriate stage, filamentous stage and young colony stage were very similar. The evolutionary relationships reflected in the developmental stages of N. sphaeroides are discussed.

Growth kinetics of 1-2 mm and 3-4 mm colonies of Nostoc sphaeroides (Cyanophyta) in outdoor culture

Nostoc sphaeroides Kutzing was cultivated in paddlewheel-driven raceway ponds and the growth kinetics of 1-2 mm and 3-4 mm colonies of N. sphaeroides was studied. The biomass productivities in 2.5 m(2) raceway ponds inoculated with 1-2 mm and 3-4 mm colonies were 5.2 and 0.25 g dry wt m(-2) stop d(-1), respectively. Furthermore, differently sized colonies showed different relative water content, total soluble carbohydrates, chlorophyll a content and density of filaments. This is the first report on mass culture of N. sphaeroides under outdoor conditions.

The accumulation and metabolism of astaxanthin in Scenedesmus obliquus (chlorophyceae)

The biosynthesis and metabolism of astaxanthin in coenobium alga Scenedesmus obliquus were investigated using a two-stage culture. The first stage was for the analysis of biosynthesis and accumulation of astaxanthin in alga cells which were cultured under induction conditions (incubation at 30 degrees C and illumination of 180 mu mol m(-2) s(-1)) for 48 h. The composition of the secondary carotenoids in algal cells was analyzed and seven ketocarotenoids were identified. The results implied that S. obliquus synthesized astaxanthin from beta-carotene through three possible pathways. In the second stage, the cultures were transferred to normal conditions (incubation at 25 C and illumination of 80 mu mol m(-2) s(-1)) for 72 h. Algal cells accumulated more chlorophyll and biosynthesis of secondary carotenoids terminated, the content of secondary carotenoids decreased from 59.48 to 6.57%. The results inferred that accumulation and metabolism of astaxanthin could be controlled by cultivated conditions which also could lead the mobilization of secondary carotenoids to support the algal cell growth. The results also implied that presumed conversions from astaxanthin to lutein or antheraxanthin could be modulated by culturing conditions. (C) 2008 Published by Elsevier Ltd.

Hybrid cytomegalovirus-U6 promoter-based plasmid vectors improve efficiency of RNA interference in zebrafish

Short hairpin RNA (shRNA) directed by RNA polymerase III (Pol III) or Pol II promoter was shown to be capable of silencing gene expression, which should permit analyses of gene functions or as a potential therapeutic tool. However, the inhibitory effect of shRNA remains problematic in fish. We demonstrated that silencing efficiency by shRNA produced from the hybrid construct composed of the CMV enhancer or entire CMV promoter placed immediately upstream of a U6 promoter. When tested the exogenous gene, silencing of an enhanced green fluorescent protein (EGFP) target gene was 89.18 +/- 5.06% for CMVE-U6 promoter group and 88.26 +/- 6.46% for CMV-U6 promoter group. To test the hybrid promoters driving shRNA efficiency against an endogenous gene, we used shRNA against no tail (NTL) gene. When vectorized in the zebrafish, the hybrid constructs strongly repressed NTL gene expression. The NTL phenotype occupied 52.09 +/- 3.06% and 51.56 +/- 3.68% for CMVE-U6 promoter and CMV-U6 promoter groups, respectively. The NTL gene expression reduced 82.17 +/- 2.96% for CMVE-U6 promoter group and 83.06 +/- 2.38% for CMV-U6 promoter group. We concluded that the CMV enhancer or entire CMV promoter locating upstream of the U6-promoter could significantly improve inhibitory effect induced by the shRNA for both exogenous and endogenous genes compared with the CMV promoter or U6 promoter alone. In contrast, the two hybrid promoter constructs had similar effects on driving shRNA.

Identification and characterization of a novel envelope protein in Rana grylio virus

Viral envelope proteins have been proposed to play significant roles in virus infection and assembly. In this study, an envelope protein gene, 53R, was cloned and characterized from Rana grylio virus (RGV), a member of the family Iridoviridae. Database searches found its homologues in all sequenced iricloviruses, and sequence alignment revealed several conserved structural features shared by virus capsid or envelope proteins: a myristoylation site, two predicted transmembrane domains and two invariant cysteine residues. Subsequently, RT-PCR and Western blot detection revealed that the transcripts encoding RGV 53R and the protein itself appeared late during infection of fathead minnow cells and that their appearance was blocked by viral DNA replication inhibitor, indicating that RGV 53R is a late expression gene. Moreover, immunofluorescence localization found an association of 53R with virus factories in RGV-infected cells, and this association was further confirmed by expressing a 53R-GFP fusion protein in pEGFP-N3/53R-transfected cells. Furthermore, detergent extraction and Western blot detection confirmed that RGV 53R was associated with virion membrane. Therefore, the current data suggest that RGV 53R is a novel viral envelope protein and that it may play an important role in virus assembly. This is thought to be the first report on a viral envelope protein that is conserved in all sequenced iridoviruses.

Population differentiation of Procypris rabaudi (Tchang) in the upper reaches of the Yangtze River revealed by mitochondrial DNA and RAPD markers

Procypris rabaudi (Tchang) is a cyprinid fish endermic to middle and upper reaches of the Yangtze River. Besides in main stream and large tributaries, there exists an early matured, small-sized ecological type in a small tributary, Tang River. In this study, mitochondrial DNA cytochrome h (cyt b) gene sequence analysis and randomly amplified polymorphic DNA (RAPD) analysis were performed to investigate the differentiation of the Tang River population from the Mudong reach population of the Yangtze River, with the purpose of conservation and exploitation of this fish. In the 1140 bps of cyt b gene sequence surveyed, 20 sites were found polymorphic, which defined 23 haplotypes. Among them, four haplotypes accounted for 54.4% of all individuals, while population-specific haplotypes occurred in low frequencies. Analysis of molecular variation on cyt b data revealed no significant partition existing between Tang River population and Mudong reach population. Analyses of 132 RAPD loci suggested that genetic variation between populations was significant, though values of different F-ST were not very high. The results revealed low genetic diversity and the beginning of population differentiation, suggesting that Tang River population should be designated as a separate Management Unit.