Sequence analysis of Arthrospira maxima based on fosmid library

Arthrospira (Spirulina) (Setchell& Gardner) is an important cyanobacterium not only in its nutritional potential but in its special biological characteristics. An unbiased fosmid library of Arthrospira maxima FACHB438 that contains 4300 clones was constructed. The size distribution of insert fragments is from 15.5 to 48.9 kb and the average size is 37.6 kb. The recombination frequency is 100%. Therefore the library is 29.9 equivalents to the Arthrospira genome size of 5.4 Mb. A total of 719 sample clones were randomly chosen from the library and 602 available sequences, which consisted of 307,547 bases, covering 5.70% of the whole genome. The codon usage of A. maxima was not strongly biased. GC content at the first position of codons (46.9%) was higher than the second (39.8%) and the third (45.5%) positions. GC content of the genome was 43.6%. Of these sequences, 287 (47.7%) showed high similarities to known genes, 63 (10.5%) to hypothetical genes and the remaining 252 (41.8%) had no significant similarities. The assigned genes were classified into 22 categories with respect to different biological roles. Remarkably, the high presence of 25 sequences (4.2%) encoding reverse transcriptase indicates the RT gene may have multiple copies in the A. maxima genome and might play an important role in the evolutionary history and metabolic regulation. In addition, the sequences encoding the ATP-binding cassette transport system and the two-component signal transduction system were the second and third most frequent genes, respectively. These genomic features provide some clues as to the mechanisms by which this organism adapts to the high concentration of bicarbonate and to the high pH environment.

Characterization and mapping of expressed sequence tags isolated from a subtracted cDNA library of Litopenaeus vannamei injected with white spot syndrome virus

A large number of polymorphic simple sequence repeats (SSRs) or microsatellites are needed to develop a genetic map for shrimp. However, developing an SSR map is very time-consuming, expensive, and most SSRs are not specifically linked to gene loci of immediate interest. We report here on our strategy to develop polymorphic markers using expressed sequence tags (ESTs) by designing primers flanking single or multiple SSRs with three or more repeats. A subtracted cDNA library was prepared using RNA from specific pathogen-free (SPF) Litopenaeus vannamei juveniles (similar to 1 g) collected before (0) and after (48 h) inoculation with the China isolate of white spot syndrome virus (WSSV). A total of 224 clones were sequenced, 194 of which were useful for homology comparisons against annotated genes in NCBI nonredundant (nr) and protein databases, providing 179 sequences encoded by nuclear DNA, 4 mitochondrial DNA, and 11 were similar to portions of WSSV genome. The nuclear sequences clustered in 43 groups, 11 of which were homologous to various ESTs of unknown function, 4 had no homology to any sequence, and 28 showed similarities to known genes of invertebrates and vertebrates, representatives of cellular metabolic processes such as calcium ion balance, cytoskeleton mRNAs, and protein synthesis. A few sequences were homologous to immune system-related (allergens) genes and two were similar to motifs of the sex-lethal gene of Drosophila. A large number of EST sequences were similar to domains of the EF-hand superfamily (Ca2+ binding motif and FRQ protein domain of myosin light chains). Single or multiple SSRs with three or more repeats were found in approximately 61 % of the 179 nuclear sequences. Primer sets were designed from 28 sequences representing 19 known or putative genes and tested for polymorphism (EST-SSR marker) in a small test panel containing 16 individuals. Ten (53%) of the 19 putative or unknown function genes were polymorphic, 4 monomorphic, and 3 either failed to satisfactorily amplify genomic DNA or the allele amplification conditions need to be further optimized. Five polymorphic ESTs were genotyped with the entire reference mapping family, two of them (actin, accession #CX535973 and shrimp allergen arginine kinase, accession #CX535999) did not amplify with all offspring of the IRMF panel suggesting presence of null alleles, and three of them amplified in most of the IRM F offspring and were used for linkage analysis. EF-hand motif of myosin light chain (accession #CX535935) was placed in ShrimpMap's linkage group 7, whereas ribosomal protein S5 (accession #CX535957) and troponin I (accession #CX535976) remained unassigned. Results indicate that (a) a large number of ESTs isolated from this cDNA library are similar to cytoskeleton mRNAs and may reflect a normal pathway of the cellular response after im infection with WSSV, and (b) primers flanking single or multiple SSRs with three or more repeats from shrimp ESTs could be an efficient approach to develop polymorphic markers useful for linkage mapping. Work is underway to map additional SSR-containing ESTs from this and other cDNA libraries as a plausible strategy to increase marker density in ShrimpMap.

Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses

Although the deep-sea sediments harbor diverse and novel bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking, considering the vast area and volume of the deep-sea sedimentary environments. Sediment bacteria vertical distribution and community structure were studied of the E272 site in the East Pacific Ocean with the molecular methods of 16S rRNA gene T-RFLP (terminal restriction fragment length polymorphism) and clone library analyses. Layered distribution of the bacterial assemblages was detected by both methods, indicating that the shallow sediments (40 cm in depth) harbored a diverse and distinct bacterial composition with fine-scale spatial heterogeneity. Substantial bacterial diversity was detected and nine major bacterial lineages were obtained, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Nitrospirae, Planctomycetes, Proteobacteria, and the candidate divisions OP8 and TM6. Three subdivisions of the Proteobacteria presented in our libraries, including the alpha-, gamma- and delta-Proteobacteria. Most of our sequences have low similarity with known bacterial 16S rRNA genes, indicating that these sequences may represent as-yet-uncultivated novel bacteria. Most of our sequences were related to the GenBank nearest neighboring sequences retrieved from marine sediments, especially from deep-sea methane seep, gas hydrate or mud volcano environments. Several sequences were related to the sequences recovered from the deep-sea hydrothermal vent or basalt glasses-bearing sediments, indicating that our deep-sea sampling site might be influenced to certain degree by the nearby hydrothermal field of the East Pacific Rise at 13A degrees N.

Tectonics of the southern tip of the Parece Vela Basin, Philippine Sea Plate

We report new geophysical and petrological data collected at the southern tip of the Parece Vela Basin in the Philippine Sea. The Parece Vela Basin, which was formed as a backarc basin behind proto Mariana arc-trench system from late Oligocene to middle Miocene, provides us a good opportunity to study the nature of successive backarc basin formations in the Philippine Sea and the relationship between are and backarc magmatisms. Regional bathymetric map derived from satellite altimetry shows that the southern tip of the basin, now located just west of the Yap arc-trench system, has unique morphological and tectonic features which include: 1) the absence of spreading center or its trace, 2) shallow average depth, and 3) enigmatic curved structures. Our newly collected high-resolution bathymetric data reveal that the spreading fabric similar to the central Parece Vela Basin exists to the north of 9 degrees 20'N. Thus it appears that the present-day Yap arc and backarc region represent the western half of the seafloor that was produced by the early E-W and the following NE-SW spreading in the northern and central Parece Vela Basin, and that the eastern counterpart now lies west of the West Mariana Ridge. Unlike the northern Parece Vela Basin, there appears to be no evidence for a systematic propagation of spreading center in the southern part. Instead two rift segments, one which extends from the central Parece Vela Basin and the other which lies within the western remnant arc (Kyushu-Palau Ridge), overlap at the southern tip of the basin, producing a complex seafloor that includes curvilinear deeps and deformed topographic highs. (c) 2007 Elsevier B.V. All rights reserved.

Modeling of a compact plate-fin reformer for methanol steam reforming in fuel cell systems

The characteristics of a compact plate-fin reformer (PFR) which integrates endothermic and exothermic reactions into one unit have been investigated by experiment as well as by numerical simulation. One reforming chamber was integrated with two vaporization chambers and two combustion chambers to constitute a single unit of PFR. In the PFR, which is based on a plate-fin beat exchanger, catalytic combustion of the reforming gas is used to simulate the fuel cell anode off gas (AOG) which supplies the necessary heat for the methanol steam reforming. Temperature distributions in all chambers and composition distribution in reforming chamber have been studied, and the effect of the ratio of H2O/CH3OH on the performance of the PFR has also been investigated. A model of the PFR was derived using a three-dimensional numerical model for a cross-current flow arrangement. Theoretical predictions of the temperature distributions in the PFR were in good agreement with experimental values. In addition, the numerical model was able to accurately predict the methanol conversion and the reformate composition in reforming chamber. © 2005 Elsevier B.V. All rights reserved.

Methanol steam reforming in a compact plate-fin reformer for fuel-cell systems

A compact plate-fin reformer (PFR) consisting of closely spaced plate-fins, in which endothermic and exothermic reactions take place in alternate chambers, has been studied. In the PFR, which was based on a plate-fin heat exchanger, catalytic combustion of the reforming gas, as a simulation of the fuel cell anode off gas (AOG), supplied the necessary heat for the reforming reaction. One reforming chamber, which was for hydrogen production, was integrated with two vaporization chambers and two combustion chambers to constitute a single unit of PFR. The PFR is very compact, easy to be placed and scaled up. The effect of the ratio of H2O/CH3OH on the performance of the PFR has been investigated, and temperature distributions in different chambers were studied. Besides, the stationary behavior of the PFR was also investigated. Heat transfer of the reformer was enhanced by internal plate-fins as well as by external catalytic combustion, which offer both high methanol conversion ratio and low CO concentration. In addition, the fully integrated reformer exhibited good test stability. Based on the PFR, a scale-up reformer was designed and operated continuously for 1000 h, with high methanol conversion ratio and low CO concentration. (c) 2004 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Evaluation of nonlinear chromatographic performance by frontal analysis using a simple multi-plate mathematical model

A multi-plate (NIP) mathematical model was proposed by frontal analysis to evaluate nonlinear chromatographic performance. One of its advantages is that the parameters may be easily calculated from experimental data. Moreover, there is a good correlation between it and the equilibrium-dispersive (E-D) or Thomas models. This shows that it can well accommodate both types of band broadening that is comprised of either diffusion-dominated processes or kinetic sorption processes. The MP model can well describe experimental breakthrough curves that were obtained from membrane affinity chromatography and column reversed-phase liquid chromatography. Furthermore, the coefficients of mass transfer may be calculated according to the relationship between the MP model and the E-D or Thomas models. (C) 2004 Elsevier B.V. All rights reserved.