Distribution of organic and reduced sulfur forms in marsh soils of coastal Louisiana

Soil samples from a Louisiana Barataria Basin brackish marshes were fractionated into acid-volatile sulfides (AVS), HCl-soluble sulfur, elemental sulfur, pyrite sulfur, ester-sulfate sulfur, and carbon-bonded sulfur. Inorganic sulfur composed 13% of total sulfur in brackish marsh soil with HCl-soluble sulfur representing 63–92% of the inorganic sulfur fraction. AVS represented less than 1% of the total sulfur pool. Pyrite sulfur and elemental sulfur together accounted for 8–33% of the inorganic sulfur pool. Organic sulfur, in the forms of ester-sulfate sulfur and carbon-bonded sulfur, was the most dominant pool representing the majority of total sulfur in brackish marsh. Results were compared to values reported for fresh and salt marshes. Reported inorganic sulfur fractions were greater in adjacent marshes, constituting 24% of total sulfur in salt marsh, and 22% in freshwater marshes. Along a salinity gradient, HCl-soluble sulfur represented 78–86% of the inorganic sulfur fraction in fresh, brackish, and salt marsh. Organic sulfur in the forms of ester-sulfate sulfur and carbon-bonded sulfur was the major constituent (76–87%) of total sulfur in all marshes. Reduced sulfur species, except elemental sulfur, increased seaward along the salinity gradient. Accumulation of reduced sulfur forms through sedimentation processes was significant in marsh energy flow in fresh, brackish and salt marshes.

Electrochemical identification of intermediate forms of urea denaturation of horse heart cytochrome c

The electrochemical identification of the urea denaturation of horse heart cytochrome c in bulk solution at the 4,4'-dithiodipyridine-modified gold electrode is reported. The results are similar to the three-step transitions of equilibrium studies (Myer et al., Biochemistry, 19 (1980) 199) of urea denaturation of cytochrome c in bulk solution. This method permits a clear resolution of which of the three steps of urea denaturation is electrochemically related. In addition, by analysing the effects of urea on the structural forms of cytochrome c and on the solution properties, as well as the cyclic voltammetric responses of the protein, the individual forms of the urea denaturation of cytochrome c can be understood. The results reflect the superposition of protein denaturation on the electrode surface and in solution.

Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta)

Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) is cultivated in China and widely consumed in Asia. To gain more insight into its physiological and biochemical properties, we generated 5318 expressed sequence tags (ESTs) from the sporophyte of P. haitanensis, and upon assembling into a nonredundant set, 2535 sequences were obtained, among which only 32.2% (816) shared certain similarity with published sequences (Nr and KOG). Functional classification of such ESTs revealed that most of the transcripts were related to its conservative biological metabolism, and P. haitanensis most likely possesses cyanide-resistant respiration and a C4-like carbon-fixation pathway, both of which have never been reported in a rhodophyte before. Twenty-eight percent of the nonredundant gene clusters exhibited significant similarity to those from P. yezoensis Ueda sporophytes, and 16 genes up-regulated in P. yezoensis sporophytes were also expressed abundantly in P. haitanensis. Codon usage analysis indicated that exposure to high GC pressure might occur during evolution of P. haitanensis. These findings represent the most extensive collection of ESTs from P. haitanensis to date, and all the ESTs in this study have been submitted to GenBank (accession nos. DN604790-DN608469, EG016226-EG018540).

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.