Latitudinal gradient of species diversity: multi-scale variability in rocky intertidal sessile assemblages along the Northwestern Pacific coast

This study examined the latitudinal gradient of species diversity of rocky intertidal sessile assemblages on the slopes of rocks along the Northwestern Pacific coast of Japan, located between 31°N and 43°N, by explicitly incorporating an hierarchical spatial scale into the monitoring design. The specific questions were to examine: (1) whether there is a latitudinal gradient of regional diversity, (2) how spatial components of the regional diversity (local diversity and turnover diversity) vary with latitude depending on spatial scale, and (3) whether the latitudinal gradient differs between different measures of species diversity, i.e. species richness and Simpsons diversity index. We measured coverage and the presence or absence of all sessile organisms in a total of 150 census plots established at five shores in each of six regions. The results showed that there were clear latitudinal gradients in regional species richness and in species turnover among shores. However, these patterns were not reflected in smaller-scale local species richness. For Simpsons diversity index, there was no evidence of latitudinal clines either in regional diversity or in spatial components. These results suggest that relative abundance of common species does not vary along latitude, while the number of rare species increases with decreasing latitude.

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An erratum to this article can be found at     

Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2

Alcanivorax is an alkane-degrading marine bacterium which propagates and becomes predominant in crude-oil-containing seawater when nitrogen and phosphorus nutrients are supplemented. To identify the genes responsible for alkane degradation in this organism, two putative genes for alkane hydroxylases were cloned from Alcanivorax borkumensis SK2. They were named alkB1 and alkB2. These genes were subsequently disrupted in A. borkumensis SK2, and the growth phenotypes of the disruptants were examined. The results indicate that the alkB1 gene is responsible for the degradation of short-chain n-alkanes. A double mutant defective in both alkB1 and alkB2 was still able to grow on medium-chain n-alkanes, indicating that genes other than alkB1 and alkB2 are also involved in n-alkane hydroxylation by A. borkumensis SK2.     

Autoxidation kinetic analysis of docosahexaenoic acid ethyl ester and docosahexaenoic triglyceride with oxygen sensor

The application of omega-3 polyunsaturated fatty acids (PUFAs) as food additives is restricted by their chemically quite reactive properties. However, quantitative analyses of the oxidative kinetics of PUFAs are very few compared to other studies on food chemistry. In this study, the autoxidation kinetics of ethyl docosahexaenoate (DHAEE), docosahexaenoic triglyceride (DHA oil), and emulsified DHA oil were investigated with an oxygen sensor. The autocatalytic reaction rate constants for DHAEE, DHA oil, and the emulsified DHA oil with 20% (w/v) GA, 20% SSPS, or 20% SSPS containing 5% soy protein were obtained at 35, 50, and 70 degrees C. A plot of the natural logarithm of the frequency factor, In ka0, vs. the activation energy, Ea, demonstrated that In ka0 against Ea fitted well with a single straight line both for the data from this study and for other reported results. This implies that the chemical compensation relationship holds between ka0 and Ea for PUFA and emulsified DHA oil.     

Effects of GroESL coexpression on the folding of nicotinoprotein formaldehyde dismutase from Pseudomonas putida F61

The overexpression of fdm, which encodes the formaldehyde dismutase from Pseudomonas putida F61, resulted in the formation of inclusion bodies made up of aggregated enzyme, leaving little activity in the soluble fraction of the transformant cells. On the other hand, coexpression of groESL along with fdm facilitated in vivo solubilization of the enzyme protein in its active form. When coexpressed with groESL, formaldehyde dismutase purified from E. coli had the same crystalline form (i.e., a regular octahedron) as the native enzyme, and like the native enzyme, it bound 1 mol of NAD(H) and 2 mol of zinc in each subunit.     

Ile (476), a constituent of di-leucine-based motif of a major lysosomal membrane protein,LGP85/LIMP II,is important for its proper distribution in late endosomes and lysosomes

Lysosomal membrane glycoprotein termed LGP85 or LIMP II extends a COOH-terminal cytoplasmic tail of R459GQGSMDEGTADERAPLIRT478, in which an L475 I476 sequence lies as a di-leucine-based motif for lysosomal targeting. In the present study, we explored the role of the I476 residue in the localization of LGP85 to the endocytic organelles using two substitution mutants called I476A and I476L in which alanine and leucine are replaced at I476, respectively, and I476R477T478-deleted LGP85 called Delta 476-478. Immunofluorescence analyses showed that I476A and I476L are largely colocalized in intracellular organelles with an endogenous late endosomal and lysosomal marker, LAMP-1, but there were some granules in which staining for the LGP85 mutants was prominent, while Delta 476-478 is detected in LAMP-1-positive and LAMP-1-negative intracellular organelles, and on the cell surface. The subcellular fractionation studies revealed that I476A, I476L, and Delta 476-478 are different from wild-type LGP85 in the distribution of early endosomes, late endosomes, and lysosomes. I476A and I476L are present more in late endosomes than in the densest lysosomes, whereas wild-type LGP85 is mainly lysosomal. Substitution of I476 for A and L differentially modified the ratios of late endosomal to lysosomal LGP85. A major portion of Delta 476-478 resided in the light buoyant density fraction containing plasma membrane and early endosomes. Taken together, these results indicate that the existence of the 476th amino acid residue is essential for localization of LGP85 to late endocytic compartments. The fact that isoleucine but not leucine is in the 476th position is especially of importance in the proper distribution of LGP85 in late endosomes and lysosomes.     

Infiltration of neutrophils following injection of apoptotic cells into the peritoneal cavity

It has been assumed that apoptosis leads to no production of pro-inflammatory cytokines or the production of anti-inflammatory cytokines in vivo, although the response of macrophages following phagocytosis of apoptotic cells in vivo has not been examined. In this study we therefore examined the response to apoptotic cells in vivo. Injection of apoptotic cells into the peritoneal cavity of mice led to transient neutrophil infiltration and concomitant production of MIP-2, a mouse homologue of IL-8. Apoptotic cells were phagocytosed by macrophages, as revealed on two-color flow cytometric analysis and microscopic observation. When the mice were depleted of macrophages by pretreatment with liposome-encapsulated dichloromethylene bisphosphonate, both neutrophil infiltration and MIP-2 production were significantly suppressed, suggesting that macrophages are required for MIP-2 production in this in vivo response. These results support the hypothesis that extensive apoptosis occurring rapidly may induce an inflammatory response in vivo.     

Biotransformation of phenanthrene and 1-methoxynaphthalene with Streptomyces lividans cells expressing a marine bacterial phenanthrene dioxygenase gene cluster

The phdABCD gene cluster in a marine bacterium Nocardioides sp. strain KP7 codes for the multicomponent enzyme phenanthrene dioxygenase. phdA encoding an iron-sulfur protein large subunit alpha, phdB encoding its small subunit beta, phdC encoding ferredoxin, and phdD encoding ferredoxin reductase, were replaced in such a way that the termination codons of the preceding open reading frames were overlapped with the initiation codons of the following genes. This manipulated phdABCD gene cluster was positioned downstream of the thiostrepton-inducible promoter PtipA in a high-copy-number vector pIJ6021, and introduced into the gram-positive, soil-inhabiting, filamentous bacterium Streptomyces lividans. The recombinant S. lividans cells converted phenanthrene into a cis-diol form, which was determined to be cis-3,4-dihydroxy-3,4-dihydrophenanthrene by its UV spectral data as well as HPLC property, using the authentic sample for comparison. This biotransformation proceeded very efficiently; 200 microM and 2 mm of phenanthrene were almost completely converted to its cis-diol form in 6 h and 32 h, respectively. In addition, the S. lividans cells carrying the phdABCD gene cluster were found to transform 1-methoxynaphthalene to two products, which were identified to be 8-methoxy-2-naphthol in addition to 8-methoxy-1,2-dihydro-1,2-naphthalenediol by their EI-MS, 1H- and 13C-NMR spectral data.