Nano‐sized bacterial magnetic particles displaying pyruvate phosphate dikinase for pyrosequencing

There is a high demand for inexpensive and high‐throughput DNA sequencing technologies in molecular biology and applied biosciences. In this study, novel nano‐sized magnetic particles displaying enzymes for pyrosequencing, a rather novel bioluminometric DNA sequencing method based on the sequencing‐by‐synthesis principle by employing a cascade of several enzymatic reactions, was developed. A highly thermostable enzyme, pyruvate phosphate dikinase (PPDK) which converts PPi to ATP was successfully expressed onto bacterial magnetic particles (BacMPs) using a novel protein display system of Magnetospirillum magneticum AMB‐1. The enzymatic stability of BacMPs displaying PPDK (PPDK‐BacMPs) to pH and temperature was evaluated and its broad range of properties was shown. Subsequently, PPDK‐BacMPs were applied in pyrosequencing and a target oligonucleotide was successfully sequenced. The PPDK enzyme displayed on BacMPs was shown to be recyclable in each sequence reaction as they can be manipulated by magnetic force. It was concluded that nano‐sized PPDK‐BacMPs are useful for the scale down of pyrosequencing reaction volumes, thus, permitting high‐throughput. The recycling of enzymes was also shown to be promising and applicable for the development of an inexpensive DNA sequencing at a low running cost. Biotechnol. Bioeng. 2009;103: 130–137. © 2008 Wiley Periodicals, Inc.     

Diverse genes of cellulase homologues of glycosyl hydrolase family 45 from the symbiotic protists in the hindgut of the termite Reticulitermes speratus

Diverse genes encoding cellulase homologues belonging to glycosyl hydrolase family 45 were identified from the symbiotic protists in the hindgut of the termite Reticulitermes speratus through the use of consensus PCR and the screening of a cDNA library. Fifteen full-length cDNA clones were isolated and sequenced, which encoded polypeptides consisting of 218–221 amino acid residues showing up to 63% identity to known family 45 cellulases. The cellulase sequences of the termite symbiotic protists were phylogenetically monophyletic, showing more than 75% amino acid identity with each other. These enzymes consist of a single catalytic domain, lacking the ancillary domains found in most microbial cellulases. By whole-cell in situ hybridization using oligonucleotide probes specific for regions conserved in some of the sequences, the origin of the genes was identified as symbiotic hypermastigote protists. The presence of diverse cellulase homologues suggests that symbiotic protists of termites may be rich reservoirs of novel cellulase sequences. Received: July 10, 2000 / Accepted: August 15, 2000     

Movement Pattern Variability in Stone Knapping: Implications for the Development of Percussive Traditions

The earliest direct evidence for tool-use by our ancestors are 2.6 million year old stone tools from Africa. These earliest artifacts show that, already, early hominins had developed the required advanced movement skills and cognitive capacities to manufacture stone tools. Currently, it is not well understood, however, which specific movement skills are required for successful stone knapping and accordingly it is unknown how these skills emerged during early hominin evolution. In particular, it is not clear which striking movements are indicative of skilled performance, how striking movement patterns vary with task and environmental constraints, and how movement patterns are passed on within social groups. The present study addresses these questions by investigating striking movement patterns and striking variability in 18 modern stone knappers (nine experienced and nine novices). The results suggest that no single movement pattern characterizes successful stone knapping. Participants showed large inter-individual movement variability of the elementary knapping action irrespective of knapping experience and knapping performance. Changes in task- and environmental constraints led knappers to adapt their elementary striking actions using a combination of individual and common strategies. Investigation of striking pattern similarities within social groups showed only partial overlap of striking patterns across related individuals. The results therefore suggest that striking movement patterns in modern stone knappers are largely specific to the individual and movement variability is not indicative of knapping performance. The implications of these results for the development of percussive traditions are discussed.     

Variations in the Chilling Sensitivity of Suspension-Cultured Cells of Mung Bean (Vigna radiata [L.] Wilczek) during the Growth Cycle

Variations in the chilling sensitivity of mung bean (Vigna radiata[L.] Wilczek) cells in suspension culture were studied withreference to the growth cycle. At the initial stages after subculture,cells were relatively insensitive to chilling, but chillingsensitivity increased abruptly thereafter and reached a maximumat the early stage of exponential growth, namely 6 days aftersubculture. Upon further culturing, cells became chilling-tolerant,becoming most tolerant at the late stage of exponential growth,namely 14–15 days after subculture. The results of thereciprocal exchange of conditioned culture medium between thecells at the early and the late exponential phases of growthprior to cold incubation revealed that the change in sensitivitywas due primarily to changes in physiological features of cellsand not to changes in the chemical composition of the culturemedium. In support of this possibility, we observed that thecold sensitivity of the tonoplast H⁺-ATPase in vivo changedmarkedly as a function of growth cycle: it was very sensitiveat the early stage of exponential growth and less sensitiveat the late stage. ¹Contribution no. 3668 from The Institute of Low TemperatureScience, Hokkaido University.     

Methane and hydrogen production in a termite-symbiont system

Methane and hydrogen emission rates and the ¹³C of CH₄ were observed for various termites in Australia, Thailand and Japan. Combined with the already reported emission rates of CH₄ in the literature, the phylogenetic trend was examined. Emission rates of the observed termites were categorized into five groups: group I with high CH₄ and low H₂ emission rates with a CH₄/H₂ ratio of typically 10/1; group II with high CH₄ and high H₂ emissions with a CH₄/H₂ ratio of 4/1–1/2; group III with low emission rates of CH₄ and H₂; group IV with high H₂ and insignificant CH₄ emissions; and group V with insignificant emissions for both CH₄ and H₂. In lower termites, there are both colonies infected and uninfected with methanogens even in the same species, and no specific trend in CH₄ and H₂ emissions was observed within a genus. Whether protozoa in the hindgut of termites are infected with methanogens or not and the differences in species compositions of protozoa are possibly responsible for the inter-colonial variations. The proportions of infected colonies were possibly small for the family Kalotermitidae (dry wood feeders), and relatively large for families of wet or damp wood feeders. The hydrogen emission rate possibly depends on the locality of methanogens: namely, whether they are intracellular symbionts of protozoa or whether they are attached to the hindgut wall. Emission rates of higher termites were classified into groups according to genera and the diet. Most species of soil or wood/soil interface feeders classified into group I, while the soil feeders Dicuspiditermes in Thailand and Amitermes in Australia were classified into groups with high H₂ emission rates. Typical wood-feeding termites and fungus-growing termites were classified into group III. The results indicate that higher termites tend to increase the CH₄ emission rate during dietary evolution from wood- to soil-feeding, and two types of the system with different efficiencies of interspecies transfer of H₂ have been formed. The ¹³C of CH₄ was discernible with a difference in the decomposition process in the termite–symbiont system among lower termites, fungus-growing termites and other higher termites.     

Light dependent activation of CO2 assimilation and the ratio of Rubisco activase to Rubisco during leaf aging of rice (Oryza sativa)

The effects of the ratio of Rubisco activase to Rubisco (activase/Rubisco ratio) on light dependent activation of CO₂ assimilation were investigated during leaf aging of rice. Changes of photosynthetic CO₂ gas exchange rates in relation to step increases of light intensity from two photon flux densities of 60 µmol m⁻² s⁻¹ (low initial PFD) and 500 µmol m⁻² s⁻¹ (high initial PFD) to saturated PFD of 1 800 µmol m⁻² s⁻¹ were measured. These photosynthetic activation processes were considered to be limited by the Rubisco activation rate when analyzed by the relaxation method. The relaxation time of low initial PFD gradually declined from 3 to 33 days after leaf emergence and showed high and negative correlation to the activase/Rubisco ratio. The initial rate of Rubisco activation under low initial PFD linearly correlated to the amounts of Rubisco activase, whereas these were almost constant from 3 to 23 days after leaf emergence. But these correlations could not be recognized in the case of high initial PFD. Moreover, the relaxation times were more sensitive to intercellular CO₂ concentration (C_i) under high initial PFD than under low initial PFD, especially, at C_i below 300 µl l⁻¹. These results suggest the involvement of the activase/Rubisco ratio in the photosynthetic activation under relatively low initial PFD, and the limitation of photosynthetic activation under relatively high initial PFD by Rubisco carbamylation during leaf aging of rice.     

Depth distribution of the percophidMatsubaraea fusiforme in Fukiagehama beach,Kyushu

Collections with a small beam trawl and push-net at Fukiagehama beach, Kyushu, revealed that individuals of the percophid,Matsubaraea fusiforme, usually inhabit water not exceeding 5 m deep along sandy beaches during warm seasons. They are especially abundant along the low water line of spring tide regardless of the tidal phase. They may over winter in the deeper waters. Their length composition suggests protandry in the species.     

A metastasis-associated antigen is present on a 60 kDa glycoprotein in transitional cell carcinoma of the human urinary bladder

Summary We have previously shown that the degree of expression of Le^x-related carbohydrate epitopes, namely,Lotus tetragonolobus agglutinin (LTA) receptors, SSEA-1 and FH6, correlates with the metastatic potential of transitional cell carcinoma of the human urinary bladder. In an effort to obtain a better reagent with which to detect a metastasis-associated epitope, monoclonal antibodies were produced against LTA receptors from BOY bladder carcinoma cells. One antigen defined by such a monoclonal antibody, MM4, indeed showed better correlation with the metastatic potential of the tumour than did other carbohydrate markers. In the LTA receptors, MM4 antigen was located only on a 60 kDa glycoprotein. In extracts from primary carcinomas and lymph node metastases, the 60 kDa glycoprotein was the principal carrier of MM4 antigen. LTA receptors from these sources were composed of arrays of glycoproteins, while the 60 kDa one was invariably present. Metastasis-associated carbohydrate epitopes on the 60 kDa glycoprotein may promote metastasis by interaction with carbohydrate-recognizing proteins such as selectins on host cells.     

Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host

We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic "termite clusters" comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.