Using the ribosomal internal transcribed spacer (ITS) as a complement marker for species identification of red macroalgae

Barcodes based on mitochondrial cytochrome oxidase (mtDNA CO1) sequences are being used for broad taxonomic groups of animals with demonstrated success in species identification and cryptic species discovery, but it has become clear that complementation by a nuclear marker system is necessary, in particular for the barcoding of plants. Here, we propose the nuclear internal transcribed spacer (ITS) as a potentially usable and complementary marker for species identification of red macroalgae, as well as present a primary workflow for species barcoding. Data show that for most red macroalgal genera (except members of the family Delesseriaceae), the size of ITS region ranges from 600 to 1200 bp, and contains enough variation to generate unique identifiers at either the species or genus levels. Consistent with previous studies, we found that the ITS sequence can resolve closely related species with the same fidelity as mtDNA CO1. Significantly, we confirmed that length polymorphism in the ITS region (including 5.8S rRNA gene) can be utilized as a character to discriminate red macroalgal species. As a complementary marker, the verifiable nuclear ITS region can speed routine identification and the detection of species, advance ecological and taxonomic inquiry, and permit rapid and accurate analysis of red macroalgae.

Halogenated Sesquiterpenes from the Marine Red Alga Laurencia saitoi (Rhodomelaceae)

Four new halogenated sesquiterpenes, 10-bromo-3-chloro-2,7-epoxychamigr-9-en-8a-of (1), 2,10 beta-dibromochamigra-2,7-dien-9 alpha-ol (2), (9S)-2-bromo-3-chloro-6,9-epoxybisabola-7(14),10-diene (3), and (9R)-2-bromo-3-chloro-6,9-epoxybisabola-7(14),10-diene (4), were characterized from the marine red alga Laurencia saitoi. In addition, two known halosesquiterpenes, 2,10-dibromo-3-chlorochamigr-7-en-9 alpha-ol (5) and isolaurenisol (6), were also isolated and identified. Their structures were established on the basis of extensive analysis of spectroscopic data.

Extra- and intra-cellular ice formation of red seabream (Pagrus major) embryos at different cooling rates

The ice crystal formation is assumed as the most lethal factor for the failure of fish embryo cryopreservation and intracellular ice formation (IIF) plays a central role in cell injury during cooling. The objectives were to observe the morphological changes of red seabream (Pagrus major) embryo during the cooling-thawing process, and to examine the effect of cryoprotectant and cooling rate on the temperatures of oil globule ice formation (T-OIF), extra-cellular ice formation (T-EIF) and intracellular ice formation (T-IIF) using cryomicroscope. After thawing, the morphological changes of embryos were observed and recorded by the video attachment and monitor under the microscope. During the cooling process, three representative phenomena were observed: oil globule gradually turned bright firstly, then the whole field of view flashed and the embryo blackened. Cooling rate affect the temperature of both extra- and intra-cellular ice formations. T-EIF and T-IIF at high cooling rate were much lower than that at low cooling rate. And the value of T-EIF - T-IIF increased from 0.45 to 11.11 degrees C with the increase of cooling rate from 3 to 130 degrees C/min. Taken together, our results suggested that high cooling rate with proper cryoprotectant would be a good option for red seabream embryo cryopreservation. (C) 2009 Elsevier Inc. All rights reserved.

In vitro antioxidative activities of extract and semi-purified fractions of the marine red alga, Rhodomela confervoides (Rhodomelaceae)

The methanol-chloroform extract of the marine red alga, Rhodomela confervoides, was measured for antioxidant activity, using the alpha,alpha-diphenyl-beta-picrylhydrazyl radical-scavenging assay and the beta-carotene-linoleate bleaching assay systems, and compared with those of the positive Controls of butylated hydroxytoluene, gallic acid and ascorbic acid, The active extract was further purified by liquid-liquid partition to afford four fractions, of which the ethyl acetate-soluble (EA) fraction exhibited the strongest antioxidant activity in both assay systems. This fraction was further divided into seven subfractions, designated as EA1-EA7, by silica gel vacuum liquid chromatography. in most cases, EA1 and EM Were found to possess the strongest activity. The total phenolic contents and reducing powers of the extract, fractions, and subfractions were also determined. Significant associations between the antioxidant potency and the total phenolic content, as well as between the antioxidant potency and the reducing power, were found for the tested fractions and subfractions. (c) 2008 Elsevier Ltd. All rights reserved.

Characterization, structure and function of linker polypeptides in phycobilisomes of cyanobacteria and red algae: An overview

Cyanobacteria and red algae have intricate light-harvesting systems comprised of phycobilisomes that are attached to the outer side of the thylakoid membrane. The phycobilisomes absorb light in the wavelength range of 500-650 nm and transfer energy to the chlorophyll for photosynthesis. Phycobilisomes, which biochemically consist of phycobiliproteins and linker polypeptides, are particularly wonderful subjects for the detailed analysis of structure and function due to their spectral properties and their various components affected by growth conditions. The linker potypeptides are believed to mediate both the assembly of phycobiliproteins into the highly ordered arrays in the phycobilisomes and the interactions between the phycobilisomes and the thylakoid membrane. Functionally, they have been reported to improve energy migration by regulating the spectral characteristics of colored phycobiliproteins. In this review, the progress regarding linker polypeptides research, including separation approaches, structures and interactions with phycobiliproteins, as well as their functions in the phycobilisomes, is presented. In addition, some problems with previous work on linkers are also discussed. (c) 2005 Elsevier B.V. All rights reserved.

Evidence for positive selection in phycoerythrin genes of red algae and cyanobacteria Prochlorococcus and Synechococcus

Because of the shortage of phycoerythrin (PE) gene sequences from rhodophytes, peBA encoding beta- and alpha-subunits of PE from three species of red algae (Ceramium boydenn, Halymenia sinensis, and Plocamium telfariae) were cloned and sequenced. Different selection forces have affected the evolution of PE lineages. 8.9 % of the codons were subject to positive selection within the PE lineages (excluding high-irradiance adapted Prochlorococcus). More than 40 % of the sites may be under positive selection, and nearly 20 % sites are weakly constraint sites in high-irradiance adapted Prochlorococcus. Sites most likely undergoing positive selection were found in the chromophore binding domains, suggesting that these sites have played important roles in environmental adaptation during PE diversification. Moreover, the heterogeneous distribution of positively selected sites along the PE gene was revealed from the comparison of low-irradiance adapted Prochlorococcus and marine Synechococcus, which firmly suggests that evolutionary patterns of PEs in these two lineages are significantly different.

Molecular cloning and expression of interleukin 1beta (IL-1 beta) from red seabream (Pagrus major)

The interleukin 1beta (IL-1beta) cDNA was cloned from the red seabream (Pagrus major) by homology cloning strategy. A cDNA fragment was amplified by PCR using two degenerated primers, which were designed according to the conserved regions of other known IL-1beta sequences, and elongated by 3' ends and 5' ends RACE PCR to get the full length coding sequence of red seabream IL-1beta (RS IL-1beta). The sequence contained 1252 nucleotides that included a 5' untranslated region (UTR) of 84 bp, a 3' UTR of 410 bp and an open reading frame (ORF) of 759 nucleotides which could be translated into a putative peptide of 253 amino acids with molecular weight of 28.6 kD and putative isoelectric point pI of 5.29. The deduced peptide contained two potential N-glycosylation sites and an identifiable IL1 family signature, but lacked the signal peptide and the clear ICE cut site, which were common in other nonmammalian IL-1beta genes. The RS IL-1beta had the highest homology with piscine IL-1beta according to phylogenetic tree analysis. The transcript expression was detected in blood, brain, gill, heart, head kidney, kidney, liver, muscle and spleen in the pathogen challenged and healthy red seabream by RTPCR. Results showed that the RS IL-1beta mRNA was constitutively expressed in most of the tissues both in stimulated and un-stimulated fish, and the expression could be enhanced by pathogen challenging.

An efficient method for DNA isolation from red algae

A simple, inexpensive and efficient method was developed for rapid isolation of total genomic DNA from 15 red algal species. It resulted in 0.1 mug high quality DNA from 1 mg fresh algal material, with an A(260)/A(280) ratio of 1.68 - 1.90. Using this rapidly isolated DNA, the 18S ribosomal RNA genes ( rDNA) and the nuclear ribosomal DNA of the internal transcribed spacer (ITS) regions were amplified. The tested DNA was suitable for restriction endonuclease digestion, genetic marker analysis and polymerase chain reaction (PCR) amplification, and may be valid for other genetic manipulation.

Tank cultivation of the red alga Palmaria palmata: Effects of intermittent light on growth rate, yield and growth kinetics

Tank cultivation of marine macroalgae involves air-agitation of the algal biomass and intermittent light conditions, i.e. periodic, short light exposure of the thalli in the range of 10 s at the water surface followed by plunging to low light or darkness at the tank bottom and recirculation back to the surface in the range of 1-2 min. Open questions relate to effects of surface irradiance on growth rate and yield in such tumble cultures and the possibility of chronic photoinhibition in full sunlight. A specially constructed shallow-depth tank combined with a dark tank allowed fast circulation times of approximately 5 s, at a density of 4.2 kg fresh weight (FW) m(-2) s(-1). Growth rate and yield of the red alga Palmaria palmata increased over a wide range of irradiances, with no signs of chronic photoinhibition, up to a growth-saturating irradiance of approximately 1600 mumol m(-2) s(-1) in yellowish light supplied by a sodium high pressure lamp at 16 h light per day. Maximum growth rate ranged at 12% FW d(-1), and maximum yield at 609 g FW m(-2) d(-1). This shows that high growth rates of individual thalli may be reached in a dense tumble culture, if high surface irradiances and short circulation times are supplied. Another aspect of intermittent light relates to possible changes of basic growth kinetics, as compared to continuous light. For this purpose on-line measurements of growth rate were performed with a daily light reduction by 50% in light-dark cycles of 1, 2 or 3 min duration during the daily light period. Growth rates at 10degreesC and 50 mumol photon m(-2) s- 1 dropped in all three intermittent light regimes during both the main light and dark periods and reached with all three periodicities approximately 50% of the control, with no apparent changes in basic growth kinetics, as compared to continuous light.

Cloning and expression of tumor necrosis factor (TNF alpha) cDNA from red seabream Pagrus major

A fragment of TNFalpha cDNA sequence from red seabream was cloned by homology cloning approach with two degenerated primers which were designed based on the conserved regions of other animals' TNF sequences. The sequence was elongated by 3' and 5' RACE to get the full length CDS sequence. This sequence contained 1264 nucleotides that included a 5' UTR of 85 bp, a 3' UTR of 514 bp and an open reading frame (ORF) of 666 bp which could encode 222 amino acids propeptide. In 3' UTR, there were several mRNA instability motifs and three endotoxin-responsive sequences, but the sequence lacked the polyadenylation signal. The deduced peptide had a clear transmembrane domain, a TNFalpha family signature and a TNF2 family profile. The cell attachment sequence and the glycosaminoglycan attachment sites were also found in the sequence. The red seabream TNF sequence shared relatively high similarity with both mammalian TNFalpha and TNFbeta by multiple sequence alignments. Phylogenetic analysis showed that the piscine TNFalpha were located independently in a different branch compared with mammalian TNFalpha and TNFbeta. Based on the primary and secondary structure analysis and gene expression study, we could concluded that the red seabream TNF should be a TNFalpha, not TNFbeta. RT-PCR was used to study TNFa transcript expression. 24 h after the red seabream was challenged by Vibrio anguillarum, the RS TNFalpha transcript expression were detected in blood, brain, gill, heart, head kidney, kidney, Ever, muscle and spleen. Results showed that TNFalpha mRNA was constitutively expressed in parts of the tissues both in stimulated and unstimulated fish and the expression could be enhanced after the pathogen infection.

Analysis of expressed sequence tags of a marine red alga, Gracilaria lemaneiformis

The expressed sequence tags (EST) has been proved to be a useful tool for discovering and identifying functional genes, especially in some species whose genetic information is unavailable. A total of 180 ESTs have been generated from a cDNA library of gametophytic Gracilaria lemaneiformis in this study. These clones are clustered into 151 groups, among which 8 groups are highly homologous to chloroplast genes and are abundant in the library. After searching for matches in the EST database of red alga, 22 groups are found to match with the registered ESTs of Rhadophyta and 6 with Gracilaria. Searching in the protein database reveal that 73 non-redundant clones have significant similarity to some known sequences, the majority of which are involved in photosynthesis, DNA transcription or translation, and 6, 4 and 3 clones are associated with growth or development, signal transduction and stress or defense response, respectively.

Isolation and purification of phycoerythrin from red alga Garcilaria verrucosa by expanded-bed-adsorption and ion-exchange chromatogaphy

R-phycoerythrin was isolated and purified from Gracilaria verrucosa on an expanded-bed adsorption column combined with ion-exchange chromatography, which can effectively solve the problem of blockage of chromatographic columns due to polysaccharides during isolation and purification of phycobiliproteins. 0.1 M (NH4)(2)SO4 proved best to elute R-phycoerythrin from the expanded-bed column, and desalted 0.1 M (NH4)(2)SO4 eluate was used on an ion-exchange column to purify the R-phycoerythrin. Using this two-stage chromatography, the purity (OD565/OD280) of the R-phycoerythrin from G. verrucosa is increased to 4.4, and the yield of purified R-phycoerythrin can reach 0.141 mg . g(-1) of the frozen alga.

Large-scale isolation and purification of R-phycoerythrin from red alga Palmaria palmata using the expanded bed adsorption method

R-phycoerythrin, a light-harvesting protein in some marine algae, and can be widely used in medicine, was isolated and purified from a red alga, Palmaria palmata (Lannaeus) Kuntze, using the streamline column (expanded bed adsorption) combined with ion-exchange chromatography. Because the crude extract was applied to the column upwardly, the column would not be blocked by polysaccharides usually very abundant in the extract of marine alga, this kind of blockage could hardly lie overcome in ordinary chromatographic column. After applying the crude extract containing 0.5 mol/L (NH4)(2)SO4, (NH4)(2)SO4 solution of different concentrations (0.2 mol/L, 0.1 mol/L and 0.05 mol/L) was used to elute the column downwardly and the eluates were collected and desalted. The desalted eluates were then applied onto all ion-exchange chromatographic column loaded with Q-sepharose for further purification of the R-phycoerythrin. Through these two steps, the purity (OD565/OD280) of the R-phycoerythrin from P. palmata was up to 3.5, more than 3.2, the commonly accepted criterion for purity, and the yield of the purified R-phycoerythrin could reach 0.122 mg/g of frozen P. palmata, much higher than that of phycobiliproteins purified with the previous methods. The result indicated that the cost of R-phycoerythrin will drop down with the method reported in this article.

In vitro assembly of R-phycoerythrin from marine red alga Polysiphonia urceolata

Scanning tunneling microscope was used to investigate the in vitro assembly of R-phycoerythrin (R-PE) from the marine red alga Polysiphonia urceolata. The results showed that R-PE molecules assembled together by disc-to-disc while absorbing on HOPG surface, which just looked like the rods in the phycobilisomes. When the water-soluble R-PE was dissolved in 2% ethanol/water spreading solution, they could form monolayer film at the air/water interface. Similar disc-to-disc array of R-PE was constituted in the two-dimensional Langmuir-Blodgett film by the external force. It could be concluded that, apart from the key role of time linker polypeptides, the in vivo assembly of phycobiliproteins into phycobilisomes is also dependent on the endogenous properties of phycobiliprotein themselves.

Integrated cultivation of the red alga Kappaphycus alvarezii and the pearl oyster Pinctada martensi

The effect of simultaneously cultivating the pearl oyster Pinctada martensi and the red alga Kappaphycus alvarezii on growth rates of both species was investigated in laboratory and field studies conducted from December 1993 to June 1995. The two study sites were in subtidal areas 100 km apart off the east coast of Hainan Island, China. Pearl oysters were cultivated in the center of an algal farm and red alga was cultivated in the center of the pearl oyster farm. These field experiments showed higher growth rates of both P. martensi and K. alvarezii in a co-culture system than in a monospecies culture system. Laboratory studies showed that the algae removed nitrogenous wastes released by pearl oysters. Algae treated with pearl oyster wastes grew much faster than those without oyster wastes. Algae treated with the seawater to which NH4Cl, NaNO3 and NaNO2 were added grew at the same rate as those treated with natural seawater containing oyster nitrogenous wastes, suggesting that enhanced growth of algae in the co-culture system was largely due to nitrogenous metabolites of the pearl oysters. In the co-culture, growth of pearl oysters was positively influenced by the presence of rapidly growing algae but when seawater temperature decreased below 20 degrees C, the algae grew slowly and there was no measurable benefit of mixed culture to either algae or pearl oyster.