Quantitative and time-course analysis of microbial degradation of 1H,1H,2H,2H,8H,8H–perfluorododecanol in activated sludge

A methylene group in the fluorinated carbon backbone of 1H,1H,2H,2H,8H,8H–perfluorododecanol (degradable telomer fluoroalcohol, DTFA) renders the molecule cleavable by microbial degradation into two fluorinated carboxylic acids. Several biodegradation products of DTFA are known, but their rates of conversion and fates in the environment have not been determined. We used liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) to quantitatively investigate DTFA biodegradation by the microbial community in activated sludge in polyethylene terephthalate (PET) flasks, which we also determined here showed least adsorption of DTFA. A reduction in DTFA concentration in the medium was accompanied by rapid increases in the concentrations of 2H,2H,8H,8H–perfluorododecanoic acid (2H,2H,8H,8H–PFDoA), 2H,8H,8H-2-perfluorododecenoic acid (2H,8H,8H-2-PFUDoA), and 2H,2H,8H-7-perfluorododecenoic acid and 2H,2H,8H-8-perfluorododecenoic acid (2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA), which were in turn followed by an increase in 6H,6H–perfluorodecanoic acid (6H,6H–PFDeA) concentration, and decreases in 2H,2H,8H,8H–PFDoA, 2H,8H,8H-2-PFUDoA, and 2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA concentrations. Accumulation of perfluorobutanoic acid (PFBA), a presumed end product of DTFA degradation, was also detected. Our quantitative and time-course study of the concentrations of these compounds reveals main routes of DTFA biodegradation, and the presence of new biodegradation pathways.

     

Challenges of reducing excess nitrogen in Japanese agroecosystems

Fertilizer N use in Japan has decreased by about 30% from 1960 to 2000, while keeping a little increase in cereal yields. This has resulted in a significant increase in apparent nitrogen use efficiency, in particular for rice. On the other hand, national N load on the environment associated with the production and consumption of domestic and imported agricultural products has almost tripled during this period, mainly due to the dramatic increase of imports of food and feedstuffs. The environmental problems, including water and air pollution, caused by the excessive loads of N are serious public concerns and there is an urgent need to minimize N losses from agricultural production. In order to meet the necessity for reducing the environmental impacts by excess N, political and technological measures have been taken at regional and country levels. In recent years, the Japanese government has embarked on a series of policies to encourage transition to an environmentally conscious agriculture. Promoting proper material circulation with reducing fertilizer impact and utilizing biomass and livestock wastes is emphasized in these policies. The effectiveness of environmental assessment and planning for reducing regional and national N load has been discussed. Implementation of environmentally friendly technologies and management, both conventional and innovational, have been developed and adopted in Japanese agriculture. The effectiveness of conventional technologies in reducing environmental reactive N has been re-evaluated. Innovative technologies, such as use of controlled availability fertilizers and livestock wastes compost pellets, are being investigated and extended. A comprehensive approach that applies political and technological measures with closer cooperation is necessary to control reactive N in the environment.     

Phospholipase D from Streptoverticillium cinnamoneum: protein engineering and application for phospholipid production

This review is focusing on an industrially important enzyme, phospholipase D (PLD), exhibiting both transphosphatidylation and hydrolytic activities for various phospholipids. The transphosphatidylation activity of PLD is particularly useful for converting phosphatidylcholine (PC) into other phospholipids. During the last decade, the genes coding for PLD have been identified from various species including mammals, plants, yeast, and bacteria. However, detailed basic and applied enzymological studies on PLD have been hampered by the low productivity in these organisms. Efficient production of a recombinant PLD has also been unsuccessful so far. We recently isolated and characterized the PLD gene from Streptoverticillium cinnamoneum, producing a secretory PLD. Furthermore, we constructed an overexpression system for the secretory enzyme in an active and soluble form using Streptomyces lividans as a host for transformation of the PLD gene. The Stv. cinnamoneum PLD was proven to be useful for the continuous and efficient production of phosphatidylethanolamine (PE) from phosphatidylcholine. Thus, the secretory PLD is a promising catalyst for synthesizing new phospholipids possessing various polar head groups that show versatile physiological functions and may be utilized in food and pharmaceutical industries.     

Sonoporation by Single-Shot Pulsed Ultrasound with Microbubbles Adjacent to Cells

In this article, membrane perforation of endothelial cells with attached microbubbles caused by exposure to single-shot short pulsed ultrasound is described, and the mechanisms of membrane damage and repair are discussed. Real-time optical observations of cell-bubble interaction during sonoporation and successive scanning electron microscope observations of the membrane damage with knowledge of bubble locations revealed production of micron-sized membrane perforations at the bubble locations. High-speed observations of the microbubbles visualized production of liquid microjets during nonuniform contraction of bubbles, indicating that the jets are responsible for cell membrane damage. The resealing process of sonoporated cells visualized using fluorescence microscopy suggested that Ca²⁺-independent and Ca²⁺-triggered resealing mechanisms were involved in the rapid resealing process. In an experimental condition in which almost all cells have one adjacent bubble, 25.4% of the cells were damaged by exposure to single-shot pulsed ultrasound, and 15.9% (∼60% of the damaged cells) were resealed within 5 s. These results demonstrate that single-shot pulsed ultrasound is sufficient to achieve sonoporation when microbubbles are attached to cells.     

Anti-oligosaccharide antibodies as tools for studying sulfated sialoglycoconjugate ligands for siglecs and selectins

Several sulfated sialoglycoconjugates have recently been shown to serve as ligands for selectins and siglecs. For instance, α2→3 sialylated 6-sulfo-Lewis x was found to serve as a ligand for selectins on skin-homing helper memory T cells, and α2→6 sialylated 6-sulfo-LacNAc to be a preferred ligand for CD22/siglec-2 on human naïve B cells. Monoclonal antibodies specific to sulfated sialoglycoconjugates are effective tools to dissect these ligands on minor subsets of human leukocytes.     

Novel Toxin-Antitoxin System Composed of Serine Protease and AAA-ATPase Homologues Determines the High Level of Stability and Incompatibility of the Tumor-Inducing Plasmid pTiC58

Stability of plant tumor-inducing (Ti) plasmids differs among strains. A high level of stability prevents basic and applied studies including the development of useful strains. The nopaline type Ti plasmid pTiC58 significantly reduces the transconjugant efficiency for incoming incompatible plasmids relative to the other type, such as octopine-type plasmids. In this study we identified a region that increases the incompatibility and stability of the plasmid. This region was located on a 4.3-kbp segment about 38 kbp downstream of the replication locus, repABC. We named two open reading frames in the segment, ietA and ietS, both of which were essential for the high level of incompatibility and stability. Plasmid stabilization by ietAS was accomplished by a toxin-antitoxin (TA) mechanism, where IetS is the toxin and IetA is the antitoxin. A database search revealed that putative IetA and IetS proteins are highly similar to AAA-ATPases and subtilisin-like serine proteases, respectively. Amino acid substitution experiments in each of the highly conserved characteristic residues, in both putative enzymes, suggested that the protease activity is essential and that ATP binding activity is important for the operation of the TA system. The ietAS-containing repABC plasmids expelled Ti plasmids even in strains which were tolerant to conventional Ti-curing treatments.Agrobacterium tumefaciens strains bearing a tumor-inducing (Ti) plasmid are the etiological agents of crown gall disease. Most genes required for pathogenicity are located on the plasmids (17, 33). Ti plasmids are kept stable at a low copy number equivalent to that of the chromosomal DNA in the bacterial cells (32) due to the repABC locus (16, 30, 34). The stability of Ti plasmids differs among strains (11).Many genes for keeping plasmids stable have been reported in eubacteria, and these are divided into three categories based on their mechanism: multimer resolution systems, active partitioning systems, and toxin-antitoxin (TA) systems (15). Multimer resolution systems increase the number of plasmid molecules by resolving a multimer plasmid into monomers, resulting in a higher probability of plasmid distribution to daughter cells during cell division even when plasmid distribution occurs randomly (29). Active partitioning systems deliver plasmid copies to each progeny cell at cell division (21). In the repABC locus, the RepA and RepB proteins and parS site(s) ensure stable plasmid inheritance by the active partitioning system (2). TA systems contribute to plasmid maintenance in cell populations by initiating growth inhibition or death of plasmid-free cells and are widely distributed among eubacterial and archaeal plasmids as well as their chromosomes (9). Generally, the TA module consists of two genes which encode toxin and antitoxin. The antitoxin neutralizes the action of a cognate toxin by interaction with the toxin or its target molecules. When a plasmid harboring the TA module is lost from a host cell, the antitoxin molecules decrease to an ineffective level because the antitoxin is degraded quickly or diluted by cell division (15). Thereafter, the toxin exerts its toxicity and inhibits the host cell growth. RNA antitoxins can suppress toxin expression by binding to the toxin mRNA as an antisense RNA or repress toxicity effects by an unknown mechanism (6, 4). In pTi-SAKURA, the Ti plasmid in the A. tumefaciens strain MAFF301001, it was shown that the tiorf24 and tiorf25 module increased plasmid stability by the TA mechanism (40; also S. Yamamoto, unpublished data).Differences in Ti plasmid stability are critical for plasmid engineering and evolution (33). However, little is known about the stability factors of Ti plasmids other than the repABC locus. In our previous study (40), tiorf24 and tiorf25 were shown to increase the segregational stability and incompatibility of Ti plasmids and reduce the efficiency of transconjugants by the introduction of incompatible plasmids into host cells. The two genes are located 2.5-kbp downstream of repABC (8). Generally, incompatibility has been defined as a situation where two plasmids contain a related replication and/or partitioning system and are unable to exist in a cell simultaneously without external selection (1). A. tumefaciens strain C58, which contains a Ti plasmid pTiC58, allows entry of an incompatible repABC plasmid into the cell 60-fold less efficiently than a derivative of C58. The derivative of C58 harbors a small repABC vector instead of pTiC58 (40). This suggests the presence of incompatibility-enhancing genes on pTiC58.In this study, we located the responsible genes in pTiC58 and found that the novel genes ietA and ietS enhance the incompatibility and stability of the plasmid by the TA mechanism.     

Function of α subunit of heterotrimeric G protein in brassinosteroid response of rice plants

The α subunit of heterotrimeric G-proteins (Gα) is involved in a broad range of aspects of the brassinosteroid (BR) response, such as the enhancement of lamina bending. However, it has been suggested from epistatic analysis of d1 and d61, which are mutants deficient for Gα and the BR receptor BRI1, that Gα and BRI1 may function via distinct pathways in many cases. In this study, we investigated further the genetic interaction between Gα and BRI1. We report the analysis of transformants of T65d1 and T65d1/d61-7 into which were introduced a constitutively active form of Gα, Q223L. The application of 24-epi-brassinolide (24-epiBL) to T65d1 expressing Q223L still resulted in elongation of the coleoptile and, in fact, it was enhanced over the wild-type plant (WT) level in a concentration dependent manner. In T65d1/d61-7 expressing Q223L, the seed size was enlarged over that of d61-7 due to activation of Gα. These results suggest that Q223L is able to augment the BR response in response to 24-epiBL and also that Q223L functions independently of BRI1 in the process of determining seed morphology, given that Q223L was functional in the BRI1-deficient mutant, d61-7.Key words: brassinosteroid, BRASSINOSTEROID INSENSITIVE1 (BRI1), genetic interaction, G-protein α subunit, rice plants, seed morphology, transgenic plants     

Extracellular and Mixotrophic Symbiosis in the Whale-Fall Mussel Adipicola pacifica: A Trend in Evolution from Extra- to Intracellular Symbiosis

Background

Deep-sea mussels harboring chemoautotrophic symbionts from hydrothermal vents and seeps are assumed to have evolved from shallow-water asymbiotic relatives by way of biogenic reducing environments such as sunken wood and whale falls. Such symbiotic associations have been well characterized in mussels collected from vents, seeps and sunken wood but in only a few from whale falls.

Methodology/Principal Finding

Here we report symbioses in the gill tissues of two mussels, Adipicola crypta and Adipicola pacifica, collected from whale-falls on the continental shelf in the northwestern Pacific. The molecular, morphological and stable isotopic characteristics of bacterial symbionts were analyzed. A single phylotype of thioautotrophic bacteria was found in A. crypta gill tissue and two distinct phylotypes of bacteria (referred to as Symbiont A and Symbiont C) in A. pacifica. Symbiont A and the A. crypta symbiont were affiliated with thioautotrophic symbionts of bathymodiolin mussels from deep-sea reducing environments, while Symbiont C was closely related to free-living heterotrophic bacteria. The symbionts in A. crypta were intracellular within epithelial cells of the apical region of the gills and were extracellular in A. pacifica. No spatial partitioning was observed between the two phylotypes in A. pacifica in fluorescence in situ hybridization experiments. Stable isotopic analyses of carbon and sulfur indicated the chemoautotrophic nature of A. crypta and mixotrophic nature of A. pacifica. Molecular phylogenetic analyses of the host mussels showed that A. crypta constituted a monophyletic clade with other intracellular symbiotic (endosymbiotic) mussels and that A. pacifica was the sister group of all endosymbiotic mussels.

Conclusions/Significance

These results strongly suggest that the symbiosis in A. pacifica is at an earlier stage in evolution than other endosymbiotic mussels. Whale falls and other modern biogenic reducing environments may act as refugia for primal chemoautotrophic symbioses between eukaryotes and prokaryotes since the extinction of ancient large marine vertebrates.     

An activated medium with high durability and low nonspecific adsorption: application to protein A chromatography

Activated media allow the user to easily synthesize a variety of affinity media. We have developed a novel activated medium based on porous silica modified with phosphorylcholine (PC) and N-hydroxysuccinimide (NHS) groups for the purpose of high-throughput purification and reducing nonspecific protein adsorption. The PC groups function as suppressors of nonspecific protein adsorption, whereas the NHS groups are able to covalently bind to the primary amino groups of ligands. Because protein A affinity medium is the most frequently used affinity medium, we prepared protein A media in which a recombinant protein A was bound to the NHS groups of the activated media and evaluated its utility. After optimizing various factors in the synthetic process, the resultant protein A medium showed improved durability at a high flow rate over 300 purification cycles and reduced nonspecific protein adsorption compared with commercially available protein A media.