Cascaded pattern formation in hydrogel medium using the polymerisation approach.

Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.

Revolving Vernier Mechanism Controls Size of Linear Homomultimer.

A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively. In summary, it is possible to affect the number of polymerization by adjusting the precise shape and movability of a molecular structure.

Triple serine loop region regulates the aspartate racemase activity of the serine/aspartate racemase family.

Recently, we cloned and characterized eleven serine and aspartate racemases (SerR and AspR, respectively) from animals. These SerRs and AspRs are not separated by their racemase functions and form a serine/aspartate racemase family cluster based on phylogenetic analysis. Moreover, we have proposed that the AspR-specific triple serine loop region at amino acid positions 150-152 may be responsible for the large AspR activity. In the present study, to test this hypothesis, we prepared and characterized fourteen mutants in this region of animal SerRs and AspRs. The large AspR activity in Acropora and Crassostrea AspR was reduced to <0.04% of wild-type after substitution of the triple serine loop region. Conversely, introducing the triple serine loop region into Acropora, Crassostrea, and Penaeus SerR drastically increased the AspR activity. Those mutants showed similar or higher substrate affinity for aspartate than serine and showed 11-683-fold higher k cat and 28-351-fold higher k cat/K m values for aspartate than serine racemization. Furthermore, we introduced serine residues in all combinations at position 150-152 in mouse SerR. These mutants revealed that a change in the enzyme function from SerR to AspR can be caused by introduction of Ser151 and Ser152, and addition of the third serine residue at position 150 further enhances the enzyme specificity for aspartate due to a decrease in the serine racemase and serine dehydratase activity. Here, we provide convincing evidence that the AspR gene has evolved from the SerR gene by acquisition of the triple serine loop region.

Distribution and evolution of the serine/aspartate racemase family in invertebrates.

Free D-amino acids have been found in various invertebrate phyla, while amino acid racemase genes have been identified in few species. The purpose of this study is to elucidate the distribution, function, and evolution of amino acid racemases in invertebrate animals. We searched the GenBank databases, and found 11 homologous serine racemase genes from eight species in eight different invertebrate phyla. The cloned genes were identified based on their maximum activity as Acropora millepora (Cnidaria) serine racemase (SerR) and aspartate racemase (AspR), Caenorhabditis elegans (Nematoda) SerR, Capitella teleta (Annelida) SerR, Crassostrea gigas (Mollusca) SerR and AspR, Dugesia japonica (Platyhelminthes) SerR, Milnesium tardigradum (Tardigrada) SerR, Penaeus monodon (Arthropoda) SerR and AspR and Strongylocentrotus purpuratus (Echinodermata) AspR. We found that Acropora, Aplysia, Capitella, Crassostrea and Penaeus had two amino acid racemase paralogous genes and these paralogous genes have evolved independently by gene duplication at their recent ancestral species. The transcriptome analyses using available SRA data and enzyme kinetic data suggested that these paralogous genes are expressed in different tissues and have different functions in vivo. Phylogenetic analyses clearly indicated that animal SerR and AspR are not separated by their particular racemase functions and form a serine/aspartate racemase family cluster. Our results revealed that SerR and AspR are more widely distributed among invertebrates than previously known. Moreover, we propose that the triple serine loop motif at amino acid positions 150-152 may be responsible for the large aspartate racemase activity and the AspR evolution from SerR.

Correction: Evaluating the impact of COVID-19 on ex-vessel prices using time-series analysis.

[This corrects the article DOI: 10.1007/s12562-021-01574-x.].

Evaluating the impact of COVID-19 on ex-vessel prices using time-series analysis.

The spread of coronavirus disease 2019 (COVID-19) and subsequent lockdown measures have impacted economies and industries worldwide. The fisheries industry witnessed a sharp decline in demand and a slump in fish prices due to its dependence on the food service industry. It is important to quantitatively assess those fish species affected most and the extent of the pandemic's impact on them, to take specific countermeasures. We propose a time-series analysis as an alternative to the current practice of using ad hoc year-on-year comparisons. Although the pandemic makes it difficult to construct a counterfactual approach due to the lack of an appropriate control group, we use time-series forecasting to simulate normal conditions using pre-pandemic data. In Tokyo, the unit price of fish species that were negatively impacted by the food services industry dropped by 12.65% to 14.64%, and by 26.08% to 28.22% after the declaration of a state of emergency. Seasonality, short weekly cycles, and short-term market trends are factors that affect the price of fish. Species-specific impact estimates related to the COVID-19 pandemic can allow policymakers to implement recovery measures in a more targeted and effective manner. The results of our analysis can increase fishers' and policymakers' awareness of the usefulness of economic analyses and incentivize them to release data to establish a system to accumulate and analyze data strategically for urgent and appropriate interventions in the fisheries industry.

Capillary electrophoresis study on the dimeric SOD enzyme in the presence of ascorbic acid.

A Notable decrease of the peak intensity of the capillary electrophoregram due to the dimeric SOD molecule was observed when a solution containing copper(II) chloride and ascorbic acid was added to the SOD solution, indicating that the capillary electrophoresis method is useful to detect the dissociation of the dimeric SOD molecule in solution, and that dissociation of the dimeric SOD molecule is induced by the presence of hydrogen peroxide. The present results may give reasonable countermeasures towards the sporadic amyotrophic lateral sclerosis in future.

Facile uptake of manganese(III) by apotransferrin: possible origin of manganism.

We have investigated the mechanism of manganese ion uptake by apo-transferrin using a capillary electrophoresis method, and obtained clear evidence that oxidation state +3 and the binuclear unit of a manganese chelate are essential factors for the facile uptake by apotransferrin, similar to that observed for Fe(III) chelates. These results may give valuable information to understand the pathogenesis of manganism and to develop new countermeasures for the neurotoxicity by manganese ions.

Diffusion modulation of DNA by toehold exchange.

We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.

Preparation of sterically protected 3,4-bis[(2,4,6-tri-tert-butylphenyl)phosphinidene]cyclobutene derivatives having ring-fused structures.

[reaction: see text] Sterically protected 3,4-diphosphinidenecyclobutenes, having ring-fused structures, were prepared. Structures of 8,9-bis[(2,4,6-tri-tert-butylphenyl)phosphinidene]bicyclo[5.2.0]non-1(7)-ene and its dichloropalladium(II) complex were analyzed by X-ray crystallography. A geometrical change induced by the complex formation was exhibited by X-ray crystallographic analysis. The geometrical change in solution was also suggested by (1)H NMR spectroscopy in CDCl(3).

A comparison of the shapes of hydroxyapatite implants before and after implantation.

Based on helical volume scan computed tomography (HVCT) data, it has been demonstrated previously that real-size models can be prepared with the binder-jet method with extremely high precision of various parts ranging from the outer structure of the cranio-maxillofacial bone to such fine parts as the cranial base and the orbital walls. The application of this method to clinical cases with large cranial bone defects has also been studied. The results showed the usefulness of the binder-jet method, employing starch for fixing, with which a model can be prepared faster and with less deformity caused by the weight of the material itself. Therefore, the binder-jet method is expected to attain greater clinical significance in this field. In this study the comparison between the shapes of implants before and after implantation revealed that the most important aspect of the design of hydroxyapatite (HAP) implants was determining the shapes of edges, especially its angles. That is, an implant needs very little trimming before being implanted to the patient's defective site if the shape of the edges of the implant can be designed and prepared to fix the incised bone surfaces properly. In addition, to obtain optimum results it was also shown that it is necessary to design optimal shapes of implants, taking into account thickness, porosity, and curvature, before processing the shapes of edges. It was found necessary to establish a technology and a method for producing HAP implants that perfectly fit cranial bone defects. For this purpose, it would be useful to make a template of the implants using the mirror-reversion and binder-jet methods.