Use of two grasses for the phytoremediation of aqueous solutions polluted with terbuthylazine

The capacity of two grasses, tall fescue (Festuca arundinacea) and orchardgrass (Dactylis glomerata), to remove terbuthylazine (TBA) from polluted solutions has been assessed in hydroponic cultures. Different TBA concentrations (0.06, 0.31, 0.62, and 1.24 mg/L) were chosen to test the capacity of the two grasses to resist the chemical. Aerial biomass, effective concentrations (to cause reductions of 10, 50, and 90% of plant aerial biomass) and chlorophylls contents of orchardgrass were found to be more affected. Tall fescue was found to be more capable of removing the TBA from the growth media. Furthermore, enzymes involved both in the herbicide detoxification and in the response to herbicide-induced oxidative stress were investigated. Glutathione S-transferase (GST, EC. 2.5.1.18) and ascorbate peroxidase (APX, EC. 1.11.1.11) of tall fescue were found to be unaffected by the chemical. GST and APX levels of orchardgrass were decreased by the treatment. These negative modulations exerted by the TBA on the enzyme of orchardgrass explained its lower capacity to cope with the negative effects of the TBA.     

An analysis of DNA replication in synchronized CHO cells treated with benzo[a]pyrene diol epoxide

Synchronized Chinese hamster ovary (CHO) cells treated with (+/-)7 beta,8 alpha- dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-dihydrobenzo[a]pyrene (BP diol epoxide I) were used to test the 'block-gap' model of replicative bypass repair in mammalian cells. One feature of the model is that carcinogenic or mutagenic DNA adducts act as blocks to the DNA replication fork on the leading strand. Using synchronized CHO cells, the rate of S phase progression by BrdUrd labeling of newly replicated DNA was measured. The rate of S phase progression was reduced by 22% and 42%, when the cells were treated at the G1/S boundary with 0.33 and 0.66 microM BP diol epoxide I, respectively. Using the pH step alkaline elution assay, it was found that the reduced rate of S phase progression was due to a delay in the appearance of multiple replicon size nascent DNA. This observation was consistent with the frequency of BP-DNA adducts present in the leading strand. A second feature of the 'block-gap' model is that the adduct-induced blockage on the lagging strand will produce gaps. It was determined by the use of high-resolution agarose gel electrophoresis, that the ligation of Okazaki size replication intermediates was blocked in a dose-dependent manner in BP diol epoxide I treated, synchronized CHO cells. These data are consistent with a block to the leading strand of DNA replication at DNA-carcinogen adducts. An inhibition of the ligation of Okazaki size fragments by BP diol epoxide I implies a block to replication of the DNA lagging strand leading to gap formation. The data presented here are, therefore, supportive of the 'block-gap' model of replicative bypass repair in carcinogen damaged mammalian cells.     

Histidine-alpha143 assists 1,2-hydroxyl group migration and protects radical intermediates in coenzyme B12-dependent diol dehydratase

Diol dehydratase of Klebsiella oxytoca contains an essential histidine residue. Its X-ray structure revealed that the migrating hydroxyl group on C2 of substrate is hydrogen-bonded to Hisalpha143. Mutant enzymes in which Hisalpha143 was mutated to another amino acid residue were expressed in Escherichia coli, purified, and examined for enzymatic activity. The Halpha143Q mutant was 34% as active as the wild-type enzyme. Halpha143A and Halpha143L showed only a trace of activity. Kinetic analyses indicated that the hydrogen bonding interaction between the hydroxyl group on C2 of substrate and the side chain of residue alpha143 is important not only for catalysis but also for protecting radical intermediates. Halpha143E and Halpha143K that did not exist as (alphabetagamma) 2 complexes were inactive. The deuterium kinetic isotope effect on the overall reaction suggested that a hydrogen abstraction step is fully rate-determining for the wild type and Halpha143Q and partially rate-determining for Halpha143A. The preference for substrate enantiomers was reversed by the Halpha143Q mutation in both substrate binding and catalysis. Upon the inactivation of the Halpha143A holoenzyme by 1,2-propanediol, cob(II)alamin without an organic radical coupling partner accumulated, 5'-deoxyadenosine was quantitatively formed from the coenzyme adenosyl group, and the apoenzyme itself was not damaged. This inactivation was thus concluded to be a mechanism-based inactivation. The holoenzyme of Halpha143Q underwent irreversible inactivation by O 2 in the absence of substrate at a much lower rate than the wild type.     

Real-time kinetic modeling of voltage-gated ion channels using dynamic clamp

We propose what to our knowledge is a new technique for modeling the kinetics of voltage-gated ion channels in a functional context, in neurons or other excitable cells. The principle is to pharmacologically block the studied channel type, and to functionally replace it with dynamic clamp, on the basis of a computational model. Then, the parameters of the model are modified in real time (manually or automatically), with the objective of matching the dynamical behavior of the cell (e.g., action potential shape and spiking frequency), but also the transient and steady-state properties of the model (e.g., those derived from voltage-clamp recordings). Through this approach, one may find a model and parameter values that explain both the observed cellular dynamics and the biophysical properties of the channel. We extensively tested the method, focusing on Na_v models. Complex Markov models (10-12 states or more) could be accurately integrated in real time at >50 kHz using the transition probability matrix, but not the explicit Euler method. The practicality of the technique was tested with experiments in raphe pacemaker neurons. Through automated real-time fitting, a Hodgkin-Huxley model could be found that reproduced well the action potential shape and the spiking frequency. Adding a virtual axonal compartment with a high density of Na_v channels further improved the action potential shape. The computational procedure was implemented in the free QuB software, running under Microsoft Windows and featuring a friendly graphical user interface.     

Archival tagging reveals swimming depth and ambient and peritoneal cavity temperature in age-0 Pacific bluefin tuna, <Emphasis Type="Italic">Thunnus orientalis</Emphasis>, off the southern coast of Japan

Although archival tags have been deployed in Thunnus since the early 1990s, few studies have placed such loggers on the small-size growth stage. In this study, Pacific bluefin tuna (PBT, Thunnus orientalis) 20–26.5 cm in fork length (FL) were fitted with archival tags and released off the southern coastal area of Japan from July to August in 2012, 2013, and 2014. Time-series data on swimming depth, ambient water temperature, and peritoneal cavity temperatures collected at 30-s intervals during 78–144 days were analyzed in 11 age-0 PBT. In August, the age-0 PBT spent 69.5 to 83.4% of their time within the mixed layer at mean temperatures between 27.6 and 28.3 °C, while previous studies reported that PBT with FL > 50 cm in the East China Sea are found most often in zones with temperatures between 14 and 19 °C. The thermal difference between the peritoneal cavity and ambient temperature was less than 1 °C for age-0 PBT in August, indicating that they were not in danger of overheating. The mean daytime swimming depths of age-0 PBT were significantly and positively correlated with the depth of the thermocline, especially from August to October. By focusing their swimming depths around the thermocline, the age-0 PBT potentially maximize the probability of encountering prey. There was a significant correlation between the mean nighttime depth and lunar illumination. The change in vertical distribution with the lunar cycle during nighttime is likely a form of predator avoidance.     

Tree‐ring analysis and modeling approaches yield contrary response of circumboreal forest productivity to climate change

Circumboreal forest ecosystems are exposed to a larger magnitude of warming in comparison with the global average, as a result of warming‐induced environmental changes. However, it is not clear how tree growth in these ecosystems responds to these changes. In this study, we investigated the sensitivity of forest productivity to climate change using ring width indices (RWI) from a tree‐ring width dataset accessed from the International Tree‐Ring Data Bank and gridded climate datasets from the Climate Research Unit. A negative relationship of RWI with summer temperature and recent reductions in RWI were typically observed in continental dry regions, such as inner Alaska and Canada, southern Europe, and the southern part of eastern Siberia. We then developed a multiple regression model with regional meteorological parameters to predict RWI, and then applied to these models to predict how tree growth will respond to twenty‐first‐century climate change (RCP8.5 scenario). The projections showed a spatial variation and future continuous reduction in tree growth in those continental dry regions. The spatial variation, however, could not be reproduced by a dynamic global vegetation model (DGVM). The DGVM projected a generally positive trend in future tree growth all over the circumboreal region. These results indicate that DGVMs may overestimate future wood net primary productivity (NPP) in continental dry regions such as these; this seems to be common feature of current DGVMs. DGVMs should be able to express the negative effect of warming on tree growth, so that they simulate the observed recent reduction in tree growth in continental dry regions.     

Identification of preferred substrate sequences for transglutaminase 1--development of a novel peptide that can efficiently detect cross-linking enzyme activity in the skin

Transglutaminase 1 (TGase 1) is an essential enzyme for cornified envelope formation in stratified squamous epithelia. This enzyme catalyzes the cross-linking of glutamine and lysine residues in structural proteins in differentiating keratinocytes. To gain insight into the preferred substrate structure of TGase 1, we used a phage-displayed random peptide library to screen primary amino acid sequences that are preferentially selected by human TGase 1. The peptides selected as glutamine donor substrate exhibited a marked tendency in primary structure, conforming to the sequence: QxK/RpsixxxWP (where x and psi represent non-conserved and hydrophobic amino acids, respectively). Using glutathione S-transferase (GST) fusion proteins of the selected peptides, we identified several sequences as preferred substrates and confirmed that they were isozyme-specific. We generated GST-fused alanine mutants of the most reactive sequence (K5) to determine the residues that were critical for reactivity. Even in peptide form, K5 appeared to have high and specific reactivity as substrate. In situ analysis of mouse skin sections using fluorescence-conjugated K5 peptide resulted in detection of TGase 1 activity with high sensitivity, but no signal was detected in a TGase 1-null mouse. In conclusion, we were successful in generating a novel substrate peptide for sensitive detection of endogenous TGase 1 activity in the skin.     

Novel Pathway for Utilization of Cyclopropanecarboxylate by Rhodococcus rhodochrous

A new strain isolated from soil utilizes cyclopropanecarboxylate as the sole source of carbon and energy and was identified as Rhodococcus rhodochrous (H. Nishihara, Y. Ochi, H. Nakano, M. Ando, and T. Toraya, J. Ferment. Bioeng. 80:400-402, 1995). A novel pathway for the utilization of cyclopropanecarboxylate, a highly strained compound, by this bacterium was investigated. Cyclopropanecarboxylate-dependent reduction of NAD⁺ in cell extracts of cyclopropanecarboxylate-grown cells was observed. When intermediates accumulated in vitro in the absence of NAD⁺ were trapped as hydroxamic acids by reaction with hydroxylamine, cyclopropanecarboxohydroxamic acid and 3-hydroxybutyrohydroxamic acid were formed. Cyclopropanecarboxyl-coenzyme A (CoA), 3-hydroxybutyryl-CoA, and crotonyl-CoA were oxidized with NAD⁺ in cell extracts, whereas methacrylyl-CoA and 3-hydroxyisobutyryl-CoA were not. When both CoA and ATP were added, organic acids corresponding to the former three CoA thioesters were also oxidized in vitro by NAD⁺, while methacrylate, 3-hydroxyisobutyrate, and 2-hydroxybutyrate were not. Therefore, it was concluded that cyclopropanecarboxylate undergoes oxidative degradation through cyclopropanecarboxyl-CoA and 3-hydroxybutyryl-CoA. The enzymes catalyzing formation and ring opening of cyclopropanecarboxyl-CoA were shown to be inducible, while other enzymes involved in the degradation were constitutive.