Genome mapping in aquatic animals: Progress and future perspectives

The genome of aquatic animals is poorly understood and information from different taxonomic groups is sketchy. While there have been intensive genomic studies on some fish models, investigations on other fishes and invertebrates have been scarce. Yet there are recently some coordinated studies on genome mapping in a number of aquaculture animals of economic importance. This review summarizes information available on genome mapping of the important fish models and aquaculture animals. The future perspectives of this field of studies are discussed.

Genome segment S8 of grass carp hemorrhage virus encodes a virion protein

The complete nucleotide sequence of the genome segment S8 of grass carp hemorrhage virus (GCHV) was determined from cDNA corresponding to the viral genomic RNA. It is 1,287 nucleotides in length and contains a large open reading frame that could encode a protein of 409 amino acids with a predicted molecular mass of 44 kD. The S8 was expressed using the pET fusion protein vector and detected by Western blotting analysis using the chicken egg IgY against intact GCHV particles, indicating that S8 encodes a virion protein. Amino acid sequence comparisons revealed that the protein encoded by S8 is closely related to protein alpha2 of mammalian reovirus, suggesting that the deduced protein of S8 is an inner capsid protein. Copyright (C) 2001 S. Karger AG, Basel.

Complete nucleotide sequence of the S10 genome segment of grass carp reovirus (GCRV)

Hemorrhagic disease, caused by the grass carp reovirus (GCRV), is one of the major diseases of grass carp in China. Little is known about the structure and function of the gene segments of this reovirus. The S10 genome segment of GCRV was cloned and the complete nucleotide sequence is reported here. The S10 is 909 nucleotides long and contains a large open reading frame (ORF) encoding a protein of 276 amino acids with a deduced molecular weight of approximately 29.7 kDa. Comparisons of the deduced amino acid sequence of GCRV S10 with those of other reoviruses revealed no significant homologies. However, GCRV S10 shared a putative zinc-finger sequence and a similar distribution of hydrophilic motifs with the outer capsid proteins encoded by Coho salmon aquareovirus (SCSV) S10, striped bass reovirus (SBRV) S10, and mammalian reovirus (MRV) S4. It was predicted that this segment gene encodes an outer capsid protein.

Studies of polysaccharides from three edible species of Nostoc (cyanobacteria) with different colony morphologies: Structural characterization and effect on the complement system of polysaccharides from Nostoc commune

The cyanobacterium Nostoc commune Vaucher produces quite complex extracellular polysaccharides. The cyanobacterium is nitrogen fixing, and on growing the cyanobacterium in media with and without nitrogen, different types of extracellular polysaccharides were obtained. These were also different from the polysaccharides present in N. commune collected in the field. High pH anion exchange chromatography (HPAEC) of weak acid hydrolysates of the culture-grown material demonstrated that, in this case, HPAEC was useful for comparison of the different polymers. The main differences between the polymers from the field group and the culture-grown samples were the presence of substantial amounts of arabinose, 2-O-methylglucose, and glucuronic acid in the latter. Methylation studies also revealed a difference in the branching points on the glucose units between the field and cultured samples, being 1,4,6 for the first and 1,3,6 for the latter. The field acidic fraction gave, on weak acid hydrolysis and separation on BioGel P2 and HPAEC, 12 oligosaccharide fractions that were isolated and studied by different mass spectroscopy techniques. The structures of the oligosaccharides were determined, and two different series that can originate from two repeating pentamers were identified: GlcAl-4/6GlcM1-4Ga11-4Glc1-4Xyl and GlcAl-4/6Glc1-4Ga11-4Glc1-4Xyl. The difference between these oligosaccharides lies in the methyl substituent on carbon 2 of the glucose unit next to the nonreducing glucuronic acid unit. The polysaccharides from field material were shown to have a strong effect on the complement system.

Sequence of genome segments 1, 2, and 3 of the grass carp reovirus (Genus Aquareovirus, family Reoviridae)

The genome segments 1, 2, and 3 of the grass carp reovirus (GCRV), a tentative species assigned to genus Aquareouirus, family Reouiridae, were sequenced. The respective segments 1, 2, and 3 were 3949, 3877, and 3702 nucleotides long. Conserved moths 5' (GUUAUUU) and 3' (UUCAUC) were found at the ends of each segment. Each segment contains a single ORF and the negative strand does not permit identification of consistent ORFs. Sequence analysis revealed that VP2 is the viral polymerase, while VPI might represent the viral guanyly/methyl transferase (involved in the capping process of RNA transcripts) and VP3 the NTPase/helicase (involved in the transcription and capping of viral RNAs), The highest amino acid identities (26-41%) were found with orthoreovirus proteins. Further genomic characterization should provide insight about the genetic relationships between GCRV, aquareoviruses, and orthoreoviruses, It should also permit to precise the taxonomic status of these different viruses. (C) 2000 Academic Press.

Characteristics of rDNA intergenic spacer region from a waterbloom cyanobacteria species Oscillatoria sp.

Sequence of rDNA intergenic spacer region (ISR) from a waterbloom cyanobacterial species Oscillatoria sp, was determined and analyzed. The results of sequence comparison showed that the spacer had a high level sequence divergence, suggesting the sequence may be a target sequence for developing cyanobacteria genus- and species-specific oligonucleotide probes. In addition, a 20bp sequence of rDNA ISR was found highly conserved in all species of cyanobacteria, which was not found in other eubacteria. This conserved sequence within a variable region indicates that it might be a functional oligonucleotide in the processing of the rRNA precursor.

Studies on polysaccharides from three edible species of Nostoc (Cyanobacteria) with different colony morphologies: Comparison of monosaccharide compositions and viscosities of polysaccharides from field colonies and suspension cultures

Hot water-soluble polysaccharides woe extracted from field colonies and suspension cultures of Nostoc commune Vaucher, Nostoc flagelliforme Berkeley et Curtis, and Nostoc sphaeroides Kutzing. Excreted extracellular polymeric substances (EPS) were isolated from the media in which the suspension cultures were grown. The main monosaccharides of the field colony polysaccharides from the three species were glucose, xylose, and galactose, with an approximate ratio of 2:1:1. Mannose was also present, but the levels varied among the species, and arabinose appeared only in N. flagelliforme. The compositions of the cellular polysaccharides and EPS from suspension cultures were more complicated than those of the field samples and varied among the different species. The polysaccharides from the cultures of N. flagelliforme had a relatively simple composition consisting of mannose, galactose, glucose, and glucuronic acid, but no xylose, as was found in the field colony polysaccharides. The polysaccharides from cultures of N. sphaeroides contained glucose (the major component), rhamnose, fucose, xylose, mannose, and galactose. These same sugars were present in the polysaccharides from cultures of N. commune, with xylose as the major component. Combined nitrogen in the media had no qualitative influence on the compositions of the cellular polysaccharides but affected those of the EPS of N. commune and N. flagelliforme. The EPS of N. sphaeroides had a very low fetal carbohydrate content and thus was not considered to be polysaccharide in nature. The field colony polysaccharides could be separated by anion exchange chromatography into neutral and acidic fractions having similar sugar compositions. Preliminary linkage analysis showed that 1) xylose, glucose, and galactose were 1-->4 linked, 2) mannose, galactose, and xylose occurred as terminal residues, and 3) branch points occurred in glucose as 1-->3,4 and 1-->3,6 linkages and in xylose as a 1-->3,4 linkage. The polymer preparations from field colonies had higher kinematic viscosities than those from corresponding suspension cultures. The high viscosities of the polymers suggested that they might DE suitable for industrial uses.

STUDIES ON MIXED MASS CULTIVATION OF ANABAENA SPP (NITROGEN-FIXING BLUE-GREEN-ALGAE, CYANOBACTERIA) ON A LARGE-SCALE

Studies on mixed mass cultivation of Anabaena spp. on a large scale (5170 m2) were conducted continuously for 3 years. Under the continental monsoon climate in northern subtropics (30-degrees-N, 115-degrees-E), 7-11 g dry weight m-2 day-1 of microalgal biomass on average was harvested in simple plastic greenhouses in the effective growth days during the warmer seasons. The maximum productivity was 22 g m-2 day-1 in the middle of summer. Observations on the productive properties of strains of Anabaena spp. indicated that they were different from and could compensate for each other in their productivities and adaptations to the seasonal changes. With different lining materials (PVC sheets, concrete, sand and soil) in the culture ponds, no significant variation of productivity was found, but bubbling with biogas in the middle of the day and the application of some growth regulating substances (2,4-D, NaHSO3 and extracts of oyster mushroom spawn) was able to improve the production. The cost of microalgal biomass in this way was around 0.75-1.0 US dollar(s) per kilogram.

Modification of two-photon excited fluorescence from quantum dots on SiN photonic crystals

We investigate two-photon excited fluorescence from CdSe quantum dots with a center-emitting wavelength of 655 nm on SiN photonic crystals. We find that two-photon excited fluorescence is enhanced by more than 1 order of magnitude in the vertical direction when a photonic crystal is used compared to the fluorescence spectra in the absence of photonic crystals. The spectrum of two-photon excited fluorescence from quantum dots on SiN photonic crystal is observed to shift to blue compared to that from quantum dots on SiN without photonic crystals. (C) 2010 Optical Society of America

Ferromagnetic modification of GaN film by Cu+ ions implantation

The structural and magnetic properties of Cu+ ions-implanted GaN films have been reported. Eighty kilo-electron-volt Cu+ ions were implanted into n-type GaN film at room temperature with fluences ranging from 1 x 10(16) to 8 x 10(16) cm(-2) and subsequently annealed at 800 degrees C for 1 h in N-2 ambient. PIXE was employed to determine the Cu-implanted content. The magnetic property was measured by the Quantum Design MPMS SQUID magnetometer. No secondary phases or clusters were detected within the sensitivity of XRD. Raman spectrum measurement showed that the Cu ions incorporated into the crystal lattice positions of GaN through substitution of Ga atoms. Apparent ferromagnetic hysteresis loops measured at 10 K were presented. The experimental result showed that the ferromagnetic signal strongly increased with Cu-implanted fluence from 1 x 10(16) to 8 x 10(16) cm(-2).

Modification of emission wavelength of self-assembled In(Ga)As/GaAs quantum dots covered by InxGa1-xAs(0 <= x <= 0.3) layer

Red shifts of emission wavelength of self-organized In(Cla)As/GaAs quantum dots (QDs) covered by 3 nm thick InxGa1-xAs layer with three different In mole fractions (x = 0.1, 0.2 and 0.3, respectively) have been observed. Transmission electron microscopy images demonstrate that the stress along growth direction in the InAs dots was reduced due to introducing the InxGa1-xAs (x = 0.1, 0.2 and 0.3) covering layer instead of GaAs layer. Atomic force microscopy pictures show a smoother surface of InAs islands covered by an In0.2Ga0.8As layer. It is explained by the calculations that the redshifts of the photoluminescence (PL) spectra from the QDs covered by the InxGa1-xAs (x greater than or equal to 0.1) layers were mainly due to the reducing of the strain other than the InAs/GaAs intermixing in the InAs QDs. The temperature dependent PL spectra further confirm that the InGaAs covering layer can effectively suppress the temperature sensitivity of PL emissions. 1.3 mum emission wavelength with a very narrow linewidth of 19.2 mcV at room temperature has been obtained successfully from In,In0.5Ga0.5As/GaAs self-assembled QDs covered by a 3-nm In0.2Ga0.2As strain reducing layer. (C) 2001 Elsevier Science B.V. All rights reserved.

Modification of InAs quantum dot structure by the growth of the capping layer

InAs quantum dots inserted at the middle of a GaAs quantum well structure have been investigated by transmission electron microscopy and scanning transmission electron microscopy. We find that the growth condition of the overlayer on the InAs dots can lead to drastic changes in the structure of the dots. We attribute the changes to a combination of factors such as preferential growth of the overlayer above the wetting layers because of the strained surfaces and to the thermal instability of the InAs dots at elevated temperature. The result suggests that controlled sublimation, through suitable manipulation of the overlayer growth conditions, can be an effective tool to improve the structure of the self-organized quantum dots and can help tailor their physical properties to any specific requirements of the device applications. (C) 1998 American Institute of Physics.