Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1

A hyperthermophilic archaeal strain, KOD1, isolated from a solfatara on Kodakara Island, Japan, has previously been reported as Pyrococcus sp. KOD1. However, a detailed phylogenetic tree, made possible by the recent accumulation of 16S rRNA sequences of various species in the order Thermococcales, indicated that strain KOD1 is a member of the genus Thermococcus. We performed DNA-DNA hybridization tests against species that displayed high similarity in terms of 16S ribosomal DNA sequences, including Thermococcus peptonophilus and Thermococcus stetteri. Hybridization results and differences in growth characteristics and substrate utilization differentiated strain KOD1 from T. peptonophilus and T. stetteri at the species level. Our results indicate that strain KOD1 represents a new species of Thermococcus, which we designate as Thermococcus kodakaraensis KOD1 sp. nov.     

Crystal structure of S-ovalbumin as a non-loop-inserted thermostabilized serpin form

Ovalbumin, a non-inhibitory member of serine proteinase inhibitors (serpin), is transformed into a heat-stabilized form, S-ovalbumin, under elevated pH conditions. The structural mechanism for the S-ovalbumin formation has long been a puzzling question in food science and serpin structural biology. On the basis of the commonly observed serpin thermostabilization by insertion of the reactive center loop into the proximal beta-sheet, the most widely accepted hypothetical model has included partial loop insertion. Here we demonstrate, for the first time, the crystal structure of S-ovalbumin at 1.9-A resolution. This structure unequivocally excludes the partial loop insertion mechanism; the overall structure, including the reactive center loop structure, is almost the same as that of native ovalbumin, except for the significant motion of the preceding loop of strand 1A away from strand 2A. The most striking finding is that Ser-164, Ser-236, and Ser-320 take the d-amino acid residue configuration. These chemical inversions can be directly related to the irreversible and stepwise nature of the transformation from native ovalbumin to S-ovalbumin. As conformational changes of the side chains, significant alternations are found in the values of the chi 1 of Phe-99 and the chi 3 of Met-241. The former conformational change leads to the decreased solvent accessibility of the hydrophobic core around Phe-99, which includes Phe-180 and Phe-378, the highly conserved residues in serpin. This may give a thermodynamic advantage to the structural stability of S-ovalbumin.     

Changes in biomass,productivity and decomposition along topographical gradients under different geological conditions in tropical lower montane forests on Mount Kinabalu,Borneo

We have examined how the structure and function of a forest ecosystem change with topography (lower-slope versus ridge) and how the changes are modified by nutrient availability depending on geological substrate (Quaternary and Tertiary sedimentary rocks and ultrabasic rock) in the tropical montane rain forests of Mt. Kinabalu (Borneo) where climate is humid and aseasonal. Reflecting the difference in site age and parent rock, the pool size of soluble-P and inorganic-N in topsoil decreased from Quaternary sedimentary >Tertiary sedimentary >ultrabasic rock on the lower-slope, and they decreased from the lower-slope to the ridge on all substrates. Forest structural attributes [stature, above-ground biomass, and leaf area index (LAI)] decreased in the order of Quaternary sedimentary >Tertiary sedimentary >ultrabasic rock in association with soil nutrients on the lower-slopes, and decreased upslope consistently on each of the three substrates. Functional attributes [above-ground net primary productivity (ANPP) and decomposition rate] demonstrated similar patterns to structure. ANPP significantly correlated with LAI among the six sites, while net assimilation rate (ANPP divided by LAI assuming an even productivity between above vs below-ground system) was nearly constant. Therefore, ANPP could be explained primarily by LAI. Topographical change in LAI could be explained by leaf mass per area (LMA) combined with stand-level leaf biomass. LMA increased upslope on all substrates in association with the decrease in individual leaf area. Stand-level leaf biomass decreased upslope on all substrates but the Tertiary sedimentary rock. Our study demonstrated that topography and geological substrates interactively affected forest structure and processes. The effect of topography on forest structure and processes was greater on nutrient-rich substrates than on poor substrates, and the effect of geological substrate was greater on lower-slopes than on ridges.     

Reduction of phosphodiesterase 3B gene expression in peroxisome proliferator-activated receptor gamma (+/-) mice independent of adipocyte size

Phosphodiesterase 3B (PDE3B) gene expression is generally reduced in large adipocytes of obese, insulin-resistant mice. This reduced gene expression is restored by peroxisome proliferator-activated receptor (PPAR) gamma ligands accompanied by a reduced fat cell size. To determine whether PDE3B gene expression is regulated by PPAR gamma itself, we analyzed lean PPAR gamma (+/-) mice with adipocyte size comparable to control PPAR gamma (+/+) mice. In adipocytes of PPAR gamma (+/-) mice, PDE3B mRNA and protein were both reduced to 63% of wild-type levels. Basal PDE activity tended to be decreased to 70% of wild-type levels, and, similarly, insulin-induced PDE activity was significantly decreased to 70%. Thus, PPAR gamma is required for PDE3B gene expression independent of adipocyte size.     

Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the alpha-Proteobacteria

A Gram-negative bacterium was previously isolated from an oil field in Shizuoka, Japan, and designated strain HD-1. Here we have performed detailed characterization of the strain, and have found that it represents a novel genus. The 16S rRNA sequence of strain HD-1 displayed highest similarity to various uncultured species (86.7-99.7%), along with 86.2-88.2% similarity to sequences from Azospirillum, Methylobacterium, Rhizobium, and Hyphomicrobium, all members of the alpha-Proteobacteria. Phylogenetic analysis revealed that HD-1 represented a deep-branched lineage among the alpha-Proteobacteria. DNA-DNA hybridization analysis with Azospirillum lipoferum and Hyphomicrobium vulgare revealed low levels of similarity among the strains. We further examined the biochemical properties of the strain under aerobic conditions. Among carbon sources, ethanol, n-propanol, n-butanol, and n-tetradecanol were the most preferred, while acetate, propionate, and pyruvate also supported high levels of growth. The strain could also grow on aromatic compounds such as toluene, benzene and phenol, and aliphatic hydrocarbons such as n-octane and n-tetradecane. In contrast, glycerol and various sugars, including glucose, fructose, maltose, and lactose, failed to support growth of HD-1. Under an anaerobic gas phase with butanol as the carbon source, little increase in cell weight was observed with the addition of several possible electron acceptors. As strain HD-1 represents a novel genus in the alpha-Proteobacteria, we designated the strain as Oleomonas sagaranensis gen. nov., sp. nov., strain HD-1.     

Morphology and physiology of the serotonin-immunoreactive putative antennal lobe feedback neuron in the male silkmoth Bombyx mori

In the male silkmoth Bombyx mori, olfactory information is relayed from olfactory receptor neurons in the antennae to the antennal lobe, and then to a variety of protocerebral neuropils. Currently, very little is known about neuromodulators that may affect the dynamics of this olfactory neural network. Immunocytochemical studies have revealed the presence of a serotonin-immunoreactive (SI) neuron that, in several insect species, is thought to provide feedback to the antennal lobe. To date, no studies have revealed details of this neuron's physiology. Using intracellular recording and staining, the silkmoth SI neuron (in two individuals) was first characterized physiologically and then stained with Lucifer Yellow to reveal morphological details. Immunocytochemical methods were also used to confirm the presence of serotonin. The silkmoth SI neuron branched in many important brain neuropils such as the mushroom body, central body, lateral accessory lobe and antennal lobe. The SI neuron in both individuals fired spontaneous, long duration action potentials, and responded to mechanosensory stimuli to the antennae.     

Structural dynamics of distal histidine replaced mutants of myoglobin accompanied with the photodissociation reaction of the ligand

Protein dynamics observed by the transient grating (TG) method are studied for some site-directed mutants at the distal histidine of myoglobin (H64L, H64Q, H64V). The time profiles of the TG signals are very sensitive to the amino acid residue of the 64 position. It was found that the sensitivity is mostly caused by the different rates of the ligand escape from the protein to solvent and the magnitude of the molecular volume change. Several molecular origins of the volume difference between MbCO and Mb, such as the electrostatic interaction in the distal pocket, movement of helices, and distal water, are proposed. Interestingly, the volume difference between the CO-trapped Mb inside the protein interior and Mb is similar to that of the partial molar volume of CO in organic solvent. The effect of mutation on the nature of the CO trapped site is discussed.     

Disassembly of amyloid beta-protein fibril by basement membrane components

Amyloid beta-protein (A3) fibril in senile plaque may be related to the pathogenesis of Alzheimer's disease (AD). Basement membrane (BM) components are associated with the plaques in AD brain. It suggests that the BM components may play an important role in the deposition of the plaque. We investigated the potential of BM components, such as type IV collagen (collagen IV) and entactin, to induce disassembly of preformed Abeta1-42 (Abeta42) fibrils in direct comparison to laminin. Thioflavin T assays revealed that these BM components disrupted preformed Abeta42 fibrils in a dose-dependent manner. The high concentration of BM components, 100 microg/mL laminin, 50 microg/mL collagen IV and 50 microg/mL entactin, had most effect on disassembly of preformed Abeta42 fibrils (Molar ratio; Abeta42:laminin = 90:1, Abeta42:collagen IV = 34:1, Abeta42:entactin = 20:1). Circular dichroism spectroscopy data indicated that the high concentration of BM components induced structural transition in Abeta42 from beta-sheet to random structures. These results suggest that collagen IV and entactin, as well as laminin, are effective inducers of disassembly of Abeta42 fibrils. The ability of these BM components to induce random structures may be linked to the disassembly of preformed Abeta42 fibrils.