Intrinsic Nature of the Ultrafast Deexcitation Pathway of Mycosporine-like Amino Acid Porphyra-334.

Porphyra-334 is a member of natural UV-screening compounds named mycosporine-like amino acids found in several marine organisms. The UV excited porphyra-334 has been identified to deexcite quickly by puckering the intramolecular cyclohexenimine ring; however, the reason for such a ring-puckering occurrence is yet unclear. In this study, we show the ring-puckering to be the relaxation pathway of the UV excited π electron which shifts from the in-ring bond to the out-of-ring bond. The ring-puckering is characterized by the torsion among the in-ring and out-of-ring bonds. Since the π electron shift is possible in two different directions at the Franck-Condon UV excited state, it enables two ring-puckering pathways: the previously reported pathway and another one newly identified at present. We also examine the ring-unpuckering pathways which are an analogy of cis/trans photoisomerization, and we find them to be not suited for the π electron shift character of the UV excited state and thus not related to the deexcitation pathway. The present study provides insight into how porphyra-334 exerts the UV-screening ability based on its cyclohexenimine ring structure.

Theoretical Study on the Kinetics of the Rubisco Carboxylase Reaction by a Model Based on Quantum Chemistry and Absolute Reaction Rate Theory.

The rate of the Rubisco carboxylase reaction is evaluated by statistical mechanics and hybrid density functional theory (DFT). The Rubisco molecular model given by Kannappan et al. was modified and used in the present calculation. The activation energies of CO2 addition reaction, H2O addition reaction, C2-C3 bond scission, and C2 protonation are estimated. We calculated the turnover number (TON) for each of the four reaction steps based on a revised absolute reaction rate theory, which became applicable to soft matter reactions. The molecular parameters used in TON calculations were obtained by DFT calculations. The TON of the total Rubisco reaction was finally evaluated using rate equations. The calculation in a vacuum gave the total TON to be around 5 × 10-5, which was much lower than the experimental value. The DFT calculation in water solvent gave the total TON to be around 0.1, which agreed reasonably well with experimentally reported values (∼2.71). The rate-limiting process was the scission reaction. The present calculation showed that both the phosphate groups in the substrate accelerate each reaction step. The present calculation showed that a more comprehensive molecular model including enolization and quantum chemical methods is necessary to make a more precise reaction model including the irreversibility of some reactions.

Molecular Design Learned from the Natural Product Porphyra-334: Molecular Generation via Chemical Variational Autoencoder versus Database Mining via Similarity Search, A Comparative Study.

A comparative study is presented. The method via chemical variational autoencoder (VAE) and the method via similarity search are compared, focusing on their generation ability for new functional molecular design. Focusing on the natural porphyra-334 as a model molecule, we generated three groups: molecules of mycosporine-like amino acids (MAAs) as seeds (G SEEDS ), molecules generated via chemical VAE (G VAE ) and molecules gathered via similarity search (G SIM ). The number of molecules that satisfy the condition for the light absorption ability of porphyra-334 in G SEEDS , G VAE , and G SIM are 52, 138, and 6, respectively. The method via chemical VAE shows a promising potential for future molecular design. By using quantum chemistry wave function properties for chemical VAE, we find new molecules that are comparable to porphyra-334, including some with unexpected geometries. At the end, we show a group of molecules found with this method.

Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami.

Environmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

Spontaneous Combustion of 2-Bromo-3-Methoxythiophene: A Study on Reaction Pathways and Energetics by Quantum Chemical Calculations.

Reaction pathways and energetics for the dimerization and trimerization reactions of 2-bromo-3-methoxythiophene (2Br-3Met) molecules are investigated using hybrid density functional theory (DFT) calculations to obtain insight into the oligomerization reaction observed in the spontaneous combustion of pure liquid 2Br-3Met. The calculations show that the carbon-bromine bond in a 2Br-3Met molecule elongates easily, and the trans addition of this C-Br bond to a double bond in the neighboring 2Br-3Met molecule occurs easily at room temperature, reflecting the evaluated activation energy of ΔHa = 12.46 kcal/mol (enthalpy) or ΔGa = 35.68 kcal/mol (Gibbs free energy, 298.150 K and 1 atm). The formation process of trimers is calculated in a similar way. A model for the explanation of spontaneous combustion is proposed; large oligomers of the 2Br-3Met molecule are produced spontaneously following the initial formation of dimers or trimers. UV-vis spectra and vibration spectra are obtained for related molecular species, which show reasonable agreement with the experimental results.

A new freshwater shrimp species of the genus Palaemon Weber, 1795 (Decapoda: Caridea: Palaemonidae) from northeastern Japan.

The palaemonid shrimp genus Palaemon Weber 1795 is currently represented by 87 species worldwide, of which 36 species inhabit freshwater environments. In this study, we describe a new species of the genus, P. septemtrionalis, primarily based on material collected from rivers in Miyagi Prefecture, Tohoku District, northeastern Japan. The present new species is morphologically and genetically close to Palaemon paucidens De Haan, 1841, but it is morphologically distinguishable from the latter by the chela of the pereopod 2 being longer than the carpus (versus shorter than the carpus in P. paucidens) and the possession of a low, laminar convexity on the flexor margin of the pereopod 3 dactylus just proximal to the base of the unguis (such a laminar structure is absent in P. paucidens). Comparison of partial sequences of the mitochondrial 16S rRNA gene supports the recognition of the new species. Examination of museum collections and a BLAST search on GenBank revealed that the geographical range of the new species includes the Sea of Japan side ranging from Hokkaido to Hyogo Prefecture and the Pacific side ranging from Aomori to Miyagi Prefecture. An identification key to the 13 Japanese species of the genus is presented.

Unique Structural Relaxations and Molecular Conformations of Porphyra-334 at the Excited State.

Quantum chemistry based simulations were used to examine the excited state of porphyra-334, one of the fundamental mycosporine-like amino acids present in a wide variety of aqueous organisms. Our calculations reveal three characteristic aspects of porphyra-334 related to either its ground or excited state. Specifically, (i) the ground state (S0) structure consists of a planar geometry in which three units can be identified, the central cyclohexene ring, the glycine branch, and the threonine branch, reflecting the π conjugation of the system; (ii) the first singlet excited state (S1) shows a large oscillator strength and a typical ππ* excitation character; and (iii) upon relaxation at S1, the originally ground state planar structure undergoes a relaxation to a nonplanar one, S1, especially at the carbon-nitrogen (CN) groups linking the cyclohexene ring to the glycine or threonine arm. The induced nonplanarity can be ascribed to the fact that the carbon atoms of the CN groups prefer an sp3 hybridization in the S1 state. At the singlet state, these processes are unlikely to be trapped by singlet-triplet intersystem crossing especially when these occur in the hydrophilic zwitter-ion forms of porphyra-334. These results provide the missing information for thorough interpretation of the stability of porphyra-334 upon UV irradiation.

Investigation of a Pathway for Water Delivery in Photosystem II Protein by Molecular Dynamics Simulation.

To understand the mechanism of the water-splitting reaction in photosynthesis, the dynamics of water molecules surrounding the oxygen evolution center (OEC) involving the Mn4O5Ca cluster in photosystem II (PSII) is investigated using molecular dynamics (MD) simulation. During the simulation, the surrounding interspace around the Mn4O5Ca cluster was filled with numerous water molecules. The traffic of water molecules in the bidirectional pathway between the Mn4O5Ca cluster and outside of PSII is investigated by analyzing MD trajectories. The result of this simulation suggests that water delivery to the Mn4O5Ca cluster in PSII is driven by self-diffusion of water molecules coupled with the synchronized motion of the residues surrounding the Mn4O5Ca cluster. By tracing these water molecules, we find that the water molecules predominantly take five water pathways to enter into and leave from PSII. In these pathways, the water molecules move being strongly affected by the structure and dynamics of PSII. Nevertheless, the directions of each water molecule in these pathways are nearly random. In contrast, the principal component analysis for Cα atoms in the PSII complex revealed that the residues surrounding the OEC showed the collective and continuing motion. In an attempt to assess the validity, the MD simulation of the D1-D61A mutant is performed, comparing the distribution of water molecules near the Mn4O5Ca cluster. The results show that the change in the water distribution by the D1-D61A mutant is responsible for the experimentally observed decrease in the activLity of PSII. The details of the pathways for water delivery provide important information about the water-splitting reaction.

Structural analysis of a novel lipooligosaccharide (LOS) from Rhodobacter azotoformans.

Lipopolysaccharides (LPS) are components of the Gram-negative bacterial cell surface that stimulate the host innate immune system through the Toll-like receptor (TLR) 4-MD-2 complex. Rhodobacter sp. have been reported to produce LPS that lack endotoxic activity, and instead act as antagonists of other endotoxins. In this report, we focused on LPS, especially the lipooligosaccharide (LOS) fraction produced by Rhodobacter azotoformans that shows production of IL-8, but has an inverse correlation with IL-6 production. We analyzed their molecular structure by using mass spectrometry and nuclear magnetic resonance spectroscopy and report a novel LOS consisting of a shorter glycan structure containing glucuronic acid but not heptoses. A novel glycan structure, Glcα(1 → 4)GlcAα(1 → 4)KDOα(2 → 4)[Glcα(1 → 5)]KDOα(2 → 6)[4-phosphate]GlcNß(1 → 6) GlcNα1-phosphate, was proposed using NMR methods. The structure was consistent with one obtained based on MS. The MS analysis further revealed the existence of structural variation caused by extension with hexoses. The acyl composition in lipid A was suggested to contain three C14 fatty acyl chains (3-OH-14:0 or 3-oxo-14:0 at N2 of GlcN-1, 3-OH-14:0 at N2 of GlcN-2, that carried another 14:1 Δ7 on its ß-hydroxyl group) and two C10 fatty acyl chains (3-OH-10:0 at O3 of both GlcN), which are same as those found in lipid A from Rhodobacter sphaeroides.

Experimental evidence on prevention of infection by the ectoparasitic protozoans Ichthyobodo salmonis and Trichodina truttae in juvenile chum salmon using ultraviolet disinfection of rearing water.

In northern Japan, juvenile chum salmon Oncorhynchus keta (Walbaum) are released from hatcheries to enhance the fishery resource. Infections with ectoparasitic protozoans, particularly the flagellate Ichthyobodo salmonis and the ciliate Trichodina truttae, occasionally cause severe mortality among hatchery-reared juveniles. This study examined the susceptibility of the two parasites to wide-ranging UV irradiation (experiment 1) and then investigated whether UV disinfection of the rearing water using a commercial device was useful for preventing infections among juveniles in a small-scale rearing system over a 28-day period (experiment 2). In experiment 1, parasite mortality reached 100% with UV irradiation doses of ≥9.60 × 105  µW s/cm2 for I. salmonis and ≥8.40 × 105  µW s/cm2 for T. truttae. In experiment 2, disinfection of the rearing water at a UV irradiation dose of 2.2 × 106  µW s/cm2 succeeded in complete prevention of both parasites in the juvenile salmon. These results elucidate the minimum dose of UV irradiation for inactivation of I. salmonis and T. truttae, and demonstrate the usefulness of water disinfection using a commercial UV irradiation device to prevent infections by these parasites in hatchery-reared juvenile chum salmon.

Effects of dietary supplementation with oregano essential oil on prevention of the ectoparasitic protozoans Ichthyobodo salmonis and Trichodina truttae in juvenile chum salmon Oncorhynchus keta.

The present study performed three experiments to establish a practical prevention strategy for the ectoparasitic flagellate Ichthyobodo salmonis and ciliate Trichodina truttae in hatchery-reared juvenile chum salmon Oncorhynchus keta using dietary supplementation with oregano essential oil. Experiment 1 showed that a diet supplemented for 3 weeks with 0.02% oregano essential oil significantly prevented infection with I. salmonis and T. truttae in juveniles reared in small tanks. Experiment 2, in outdoor hatchery ponds, demonstrated that the oregano treatment completely prevented I. salmonis infection for 52 days and T. truttae infection for 38 days. Oregano-treated juvenile mortality attributable to infection with these protozoans also decreased to 7.6% of control juvenile mortality, confirming the utility of this treatment in cultured O. keta. Physiological analyses of the oregano-treated juveniles elucidated the treatment's safety in relation to their metabolism, osmoregulation, natural immunity and olfactory responses and also detected carvacrol (a major component of oregano essential oil which shows antimicrobial activity) on the skin. In experiment 3, exposure of the two protozoans to oregano essential oil revealed a weak antiparasitic action on the body surface of the juvenile O. keta. The overall results demonstrate that dietary oregano supplementation is a practical prevention strategy for I. salmonis and T. truttae in hatchery-reared juvenile O. keta and suggest the possibility that its anti-parasitic action is attributable to a component of the oil that emerges onto the skin of the body of the fish.

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

The octanol-water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values.

Epizootiology of the ectoparasitic protozoans Ichthyobodo salmonis and Trichodina truttae on wild chum salmon Oncorhynchus keta.

Infestations of the ectoparasitic flagellate Ichthyobodo salmonis and the ciliate Trichodina truttae have caused acute mortalities of hatchery-reared juvenile chum salmon Oncorhynchus keta in Hokkaido, northern Japan. This study examined the epizootiology of I. salmonis and T. truttae on wild chum salmon as a possible infection source of the 2 parasitic protozoans in hatcheries. Infestations by both ectoparasites were detected on freshwater-adapted adult and juvenile chum salmon in all 4 rivers examined. This is the first study of an anadromous Pacific salmonid to report infestation of I. salmonis and T. truttae in adults returning for spawning. Among the marine-inhabiting phase of chum salmon, infestation with I. salmonis, but not T. truttae, was observed on adults and juveniles. The 2 protozoans were experimentally transmitted at the same time from wild to hatchery-reared chum salmon juveniles, and caused a high rate of mortality in the hatchery fish. In freshwater, the proliferation rate of T. truttae was greater than that of I. salmonis. These observations show that the euryhaline ectoparasite I. salmonis can infest chum salmon throughout their life cycle, in both river and ocean habitats, whereas T. truttae is able to infest these salmonids only in freshwater. Furthermore, wild chum salmon were shown to be a potential infestation source for both T. truttae and I. salmonis in hatchery fish.

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

In this study, three reaction mechanisms of a benzyne-nickel (Ni) complex ([Ni(C6H4)(dcpe)]) with iodomethane during the methylation process were investigated, namely (a) SN2 reaction of the benzyne-Ni complex with iodomethane, (b) concerted σ-bond metathesis during the bond breaking/forming processes, and (c) oxidative addition of iodomethane to the Ni-center and the subsequent reductive elimination process. DFT calculations revealed that the reaction barrier of the SN2 reaction is slightly lower than those of the other mechanisms. The results of orbital analyses suggest that [Ni(C6H4)(dcpe)] forms a metallacycle structure between benzyne and the NiII (3d8) center instead of the η2-structure with the Ni0 (3d10) center. The metallacycle structures became inappropriate as the intermediates of oxidative addition in the formation of the NiII-Me bond, avoiding further oxidation to the high-valent NiIV. The high free energy along σ-bond metathesis was generated from the steric hindrance, thus invoking methylation and Ni-I bond formation concertedly.

How seaweeds release the excess energy from sunlight to surrounding sea water.

We report an atomistic insight into the mechanism regulating the energy released by a porphyra-334 molecule, the ubiquitous photosensitive component of marine algae, in a liquid water environment upon an electron excitation. To quantify this rapidly occurring process, we resort to the Fourier analysis of the mass-weighted auto-correlation function, providing evidence for a remarkable dynamic change in the number of hydrogen bonds among water molecules and between the porphyra-334 and its surrounding hydrating water. Hydrogen bonds between the porphyra-334 and close by water molecules can act directly and rather easily to promote an efficient transfer of the excess kinetic energies of the porphyra-334 to the surrounding solvating water molecules via an activation of the collective modes identified as hydrogen-bond stretching modes in liquid water which eventually results in a disruption of the hydrogen bond network. Since porphyra-334 is present in seaweeds, aquatic cyanobacteria (blue-green algae) and red algae, our findings allow addressing the question how algae in oceans or lakes, upon sunlight absorption, can release large amounts of energy into surrounding water without destabilizing neither their own nor the H2O molecular structure.

Recovery of Coastal Fauna after the 2011 Tsunami in Japan as Determined by Bimonthly Underwater Visual Censuses Conducted over Five Years.

Massive tsunamis induce catastrophic disturbance in marine ecosystems, yet they can provide unique opportunities to observe the process of regeneration. Here, we report the recovery of fauna after the 2011 tsunami in northeast Japan based on underwater visual censuses performed every two months over five years. Both total fish abundance and species richness increased from the first to the second year after the tsunami followed by stabilization in the following years. Short-lived fish, such as the banded goby Pterogobius elapoides, were relatively abundant in the first two years, whereas long-lived species, such as the black rockfish Sebastes cheni, increased in the latter half of the survey period. Tropical fish species were recorded only in the second and third years after the tsunami. The body size of long-lived fish increased during the survey period resulting in a gradual increase of total fish biomass. The recovery of fish assemblages was slow at one site located in the inner bay, where the impact of the tsunami was the strongest. Apart from fish, blooms of the moon jellyfish Aurelia sp. occurred only in the first two years after the tsunami, whereas the abundances of sea cucumber Apostichopus japonicus and abalone Haliotis discus hannai increased after the second year. Although we lack quantitative data prior to the tsunami, we conclude that it takes approximately three years for coastal reef fish assemblages to recover from a heavy disturbance such as a tsunami and that the recovery is dependent on species-specific life span and habitat.

Legitimate intermediates of oxygen evolution on iridium oxide revealed by in situ electrochemical evanescent wave spectroscopy.

Understanding how the four-electron oxidation of water to dioxygen proceeds in different materials is critical to the rational design of efficient catalysts towards artificial photosynthetic systems. Here, using in situ electrochemical evanescent wave spectroscopy under oxygen-evolving conditions, we report two intermediates of iridium oxide (IrOx), which is the most active and stable catalyst characterized to date in acidic medium. The observed potential dependence of the two intermediates indicated that they were associated with different surface sites, and intermediate scavenging experiments using H2O2 provided insight into their role during catalysis. Notably, an Ir(V) species with an absorption maximum at 450 nm was found to mediate the initial two-electron oxidation of water. Inhibition of the Ir(V) species by H2O2, combined with computational modeling, indicates that the accumulation and concurrent spin-state change of the Ir(V) species is a prerequisite for efficient water oxidation by IrOx electrodes.

Structural Changes Correlated with Magnetic Spin State Isomorphism in the S2 State of the Mn4CaO5 Cluster in the Oxygen-Evolving Complex of Photosystem II.

The Mn4CaO5 cluster in Photosystem II catalyzes the four-electron redox reaction of water oxidation in natural photosynthesis. This catalytic reaction cycles through four intermediate states (Si, i = 0 to 4), involving changes in the redox state of the four Mn atoms in the cluster. Recent studies suggest the presence and importance of isomorphous structures within the same redox/intermediate S-state. It is highly likely that geometric and electronic structural flexibility play a role in the catalytic mechanism. Among the catalytic intermediates that have been identified experimentally thus far, there is clear evidence of such isomorphism in the S2 state, with a high-spin (5/2) (HS) and a low spin (1/2) (LS) form, identified and characterized by their distinct electron paramagnetic resonance (EPR spectroscopy) signals. We studied these two S2 isomers with Mn extended X-ray absorption fine structure (EXAFS) and absorption and emission spectroscopy (XANES/XES) to characterize the structural and electronic structural properties. The geometric and electronic structure of the HS and LS S2 states are different as determined using Mn EXAFS and XANES/XES, respectively. The Mn K-edge XANES and XES for the HS form are different from the LS and indicate a slightly lower positive charge on the Mn atoms compared to the LS form. Based on the EXAFS results which are clearly different, we propose possible structural differences between the two spin states. Such structural and magnetic redox-isomers if present at room temperature, will likely play a role in the mechanism for water-exchange/oxidation in photosynthesis.

Structural changes in the S3 state of the oxygen evolving complex in photosystem II.

The S3 state of the Mn4 CaO5 -cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S2 to S3 transition that becomes a substrate water, we examined if the water insertion is essential for the S3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S3 stage. The novel S3 state structure consisting of only short 2.7-2.8 Å Mn-Mn distances was discussed.

Activation of CO2 by ionic liquid EMIM-BF4 in the electrochemical system: a theoretical study.

The electrochemical reduction of CO2 to CO by an ionic liquid EMIM-BF4 is one of the most promising CO2 reduction processes proposed so far with its high Faradaic efficiency and low overpotential. However, the details of the reaction mechanism are still unknown due to the absence of fundamental understandings. In this study, the most probable and stable geometries of EMIM-BF4 and CO2 were calculated by quantum chemistry in combination with exhaustive search. A possible reaction pathway from CO2 to CO catalyzed by EMIM-BF4, including the most plausible intermediates and the corresponding transition states, was proposed. The role of EMIM-BF4 is explained as forming a complex of [EMIM-COOH](-) with CO2 followed by decomposing to CO.