Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

Using a combined computational program. we identified 50 potential microRNAs (miRNAs) in Giardia lamblia. one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs.

Biodiversity values of different aquatic systems, habitats and organisms in relation to restoration and sustaining of biodiversity

Biodiversity values provide objective data and advice from which policy makes could assess the conservation options and determine optimal policies that would balance the needs of conservation with the socia-economic needs of the people in the area.

Physiological comparison between colonial and unicellular forms of Microcystis aeruginosa Kutz. (Cyanobacteria)

In order to gain insight into the bloom sustainment of colonial Microcystis aeruginosa Katz., physiological characterizations were undertaken in this study. Compared with unicellular Microcystis, colonial Microcystis phenotypes exhibited a higher maximum photosynthetic rate (Pm), a higher maximum electron transfer rate (ETRmax), higher phycocyanin content, and a higher affinity for inorganic carbon (K-0.5 DIC <= 8.4 +/- 0.7 mu M) during the growth period monitored in this study. This suggests that photosynthetic efficiency is a dominant physiological adaptation found in colonial Microcystis, thus promoting bloom sustainment. In addition, the high content of soluble and total carbohydrates in colonial Microcystis suggests that this phenotype may possess a higher ability to tolerate enhanced stress conditions when compared to unicellular (noncolonial) phenotypes. Therefore, high photosynthetic activities and high tolerance abilities may explain the bloom sustainment of colonial Microcystis in eutrophic lakes.

Optimization of growth and fatty acid composition of a unicellular marine picoplankton, Nannochloropsis sp., with enriched carbon sources

A unicellular marine picoplankton, Nannochloropsis sp., was grown under CO2-enriched photoautotrophic or/and acetate-added mixotrophic conditions. Photoautotrophic conditions with enriched CO2 of 2800 mul CO2 l(-1) and aeration gave the highest biomass yield (634 mg dry wt l(-1)), the highest total lipid content (9% of dry wt), total fatty acids (64 mg g(-1) dry wt), polyunsaturated fatty acids (35% total fatty acids) and eicosapentaenoic acid (EPA, 20:5omega3) (16 mg g(-1) dry wt or 25% of total fatty acids). Mixotrophic cultures gave a greater protein content but less carbohydrates. Adding sodium acetate (2 mM) decreased the amounts of the total fatty acids and EPA. Elevation of CO2 in photoautotrophic culture thus enhances growth and raises the production of EPA in Nannochloropsis sp.

The comparative estimation of phytoplanktonic, microphytobenthic and macrophytobenthic primary production in the oceans

The contributions of the planktonic unicellular algae [phytoplankton), the benthic unicellular algae [microphytobenthos) and the benthic multicellular algae (macrophytobenthos) to the primary production of the world ocean are evaluated, together with the respective limitations regarding data, concepts and methods. The use of “free-water” methods (e.g. in situ oxygen or CO2 budgets) is recommended in complement to the more specific measurements on enclosed organisms. For phytoplankton, a previous estimate of 30 . lo9 t C y-’ is retained as a minimal estimate. Earlier estimates of the world benthic production have been based on indirect calculations; revised estimates are suggested here which still lack precision but rely on the actual measurements available at present. Primary production of the micro- and macrobenthic algae amount to 50 and 375 g C m-? y-’ respectively as averages for the whole photic layer they can colonize, and total 2.9 . 10‘ t C y-’ for the world ocean. Thus, benthic algae contribute some 10% of the total marine primary production. On the continental shelf alone, the contributions of benthic and planktonib algae are commensurate and nearly equivalent.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Transient expression of lacZ in bombarded unicellular green alga Haematococcus pluvialis

This paper reports for the first time the transient expression of a reporter gene, LacZ, in the unicellular green alga Haematococcus pluvialis. By employing the micro-particle bombardment method, motile cells in the exponential phase showed transient expression of lacZ. This was detected in bombarded motile cells under the rupture-disc pressures of 3103 KPa and 4137 KPa. Transient expression of LacZ gene could not be observed in non-motile cells of this alga under the same transformation condition. No LacZ background was found in either the motile cells or the non-motile cells. The study suggests a promising potential of the SV40 promoter and the lacZ reporter gene in genetic engineering of unicellular green algae.

Diversity of pigment-protein complexes of photosynthetic organisms.

PS I, PS II and light-harvesting complexes (LHC) in oxygen evolving photosynthetic organisms were reviewed. These organisms include cyanobacteria, red algae, brown algae, diatoms, chrysophytes, dinophytes, xanthophytes, crypophytes, green algae and green plants. The diversity of pigment-protein complexes that fuel the conversion of radiant energy to chemical bond energy was highlighted, and the evolutionary relationships among the LHC structural polypeptides and the characteristics of the fluorescence emission of PS I at 77 K was discussed.

MARINE ORGANISMS ATTACHED TO SEAWEED SURFACES IN JIAOZHOU BAY, CHINA

Scanning electron microscopy of the surfaces of the seaweeds Laminaria japonica, haploid Porphyra yezoensis, Ulva pertusa and the diploid conchocelis of P. yezoensis and P. haitanensis revealed Vibrio and Micrococcus to be abundant on the surfaces of U. pertusa and P. yezoensis. Vibrio, Flavobacterium, Pseudomonas, Staphylococcus, Bacillus, Corynebacterium and other genera were isolated from the surfaces of L. japonica.

Carbon isotopic studies of individual lipids in organisms from the Nansha sea area, China

Carbon isotopes of individual lipids in typical organisms from the Nansha sea area were measured by the GC-IRMS analytical technique. delta(13)C values of saturated fatty acids in different organisms examined are from -25.6parts per thousand to -29.7parts per thousand with the average values ranging from -26.4parts per thousand to -28.2parts per thousand and the variance range of 11.8parts per thousand, between different organisms is also observed. Unsaturated fatty acids have heavy carbon isotopic compositions and the mean differences of 2.9%.9-6.8parts per thousand compared to the same carbon number saturated fatty acids. delta(13)C values of n-alkanes range from -27.5%o to -29.7parts per thousand and their mean values, ranging from -28.6parts per thousand, to -28.9parts per thousand, are very close in different organisms. The mean difference in delta(13)C between the saturated fatty acids and n-alkanes is only 1.5parts per thousand, indicating that they have similar biosynthetic pathways. The carbon isotopic variations between the different carbon-number lipids are mostly within +/-2.0parts per thousand, reflecting that they experienced a biosynthetic process of the carbon chain elongation. At the same time, the carbon isotopic genetic relationships between the biological and sedimentary lipids are established by comparative studies of carbon isotopic compositions of individual lipids in organisms and sediments from the Nansha sea area, which provides scientific basis for carbon isotopic applied research of individual lipids.

Comparison of effectiveness of different ashing auxiliaries for determination of phosphorus in natural waters, aquatic organisms and sediments by ignition method

An improved method for the determination of phosphorus in natural waters, aquatic organisms and sediments by ignition method is proposed. The recoveries of phosphorus (P) from selected inorganic and organic P-containing compound standards after ignition with different auxiliaries, such as MgSO4, Mg(NO3)(2), MgO2, Mg(Ac-2) and CaCl2, were compared. We found that the phosphorus from most compound standards could not be completely recovered when these compounds were ignited (450-500degreesC) with the MgSO4 as auxiliary and the baked residue was extracted with 0.2 mol l(-1) HCl for 30min at 80degreesC or at room temperature. P recoveries, for example, were poor, less than 85%, if pyrophosphate and metaphosphate were ignited with the addition Of MgSO4 prior to the extraction of the baked residue with 0.2 mol l(-1) HCl at 80degreesC for 30 min. In contrast, MgO2, Mg(Ac)(2) and CaCl2, as well as Mg(NO3)(2), could all yield complete P recoveries at routine ashing temperatures (450-500degreesC). The results demonstrate that MgC12 is a more effective auxiliary agent for the determination of phosphorus in natural waters, aquatic organisms and sediments by ignition method than MgSO4 which is commonly used. (C) 2003 Elsevier Science Ltd. All rights reserved.

Clay surface modification and its coagulation of red tide organisms

Surface modification of montmorillonite by means of Mg2+ insertion reaction has been studied and a positively charged montmorillonite has been prepared. The effects of preparation temperature and Mg2+ concentration on the positive charge property of the clay and on the clay coagulating Heterosigma akashiwo have been studied. The results showed that the modified clay enhanced the coagulation and the used amount decreased to 1/5-1/10 of the original. The removal rates of Heterosigma akashiwo were correlated positively with positive charge on the clay in accordance with theoretical model.

Identification of ribosomal proteins specific to higher eukaryotic organisms

This report describes the identification of a novel protein named PS1D (Genbank accession number ), which is composed of an S1-like RNA-binding domain, a (cysteine)x3-(histidine) CCCH-zinc finger, and a very basic carboxyl domain. PS1D is expressed as two isoforms, probably resulting from the alternative splicing of mRNA. The long PS1D isoform differs from the short one by the presence of 48 additional amino acids at its amino-terminal extremity. Analysis of PS1D subcellular distribution by cell fractionation reveals that this protein belongs to the core of the eukaryotic 60S ribosomal subunit. Interestingly, PS1D protein is a highly conserved protein among mammalians as murine, human, and simian PS1D homologues share more than 95% identity. In contrast, no homologous protein is found in lower eukaryotes such as yeast and Caenorhabditis elegans. These observations indicate that PS1D is the first eukaryotic ribosomal protein that is specific to higher eukaryotes.