Complete mitochondrial DNA sequence of a tadpole shrimp (Triops cancriformis) and analysis of museum samples

The complete mitochondrial DNA (mtNDA) of the tadpole shrimp Triops cancriformis was sequenced. The sequence consisted of 15,101 bp with an A+T content of 69%. Its gene arrangement was identical with those sequences of the water flea (Daphnia pulex) and giant tiger prawn (Penaeus monodon), whereas it differed from that of the brine shrimp (Artemia franciscana) in the arrangement of its genes for tRNAs. Phylogenetic analysis revealed T. cancriformis to be more closely related to the water flea than to the brine shrimp and giant tiger prawn. We also compared the 16S rRNA sequences of five formalin-fixed tadpole shrimps that had been collected in five different locations and stored in a museum. The sequence divergence was in the range of 0-1.51%, suggesting that those samples were closely related to each other.     

Photoresponsive rolling and bending of thin crystals of chiral diarylethenes

Dithienylhexafluorocyclopentene with (R)- or (S)-N-phenylethylamide substituents formed rod-like and 0.2-1.0 microm-thick platelike crystals by sublimation; upon UV irradiation, the crystals bent concavely to the incident light and finally rolled crystals were obtained; the bent crystals were reconverted to flat crystals by visible light irradiation.     

Photochromism of diarylethene single molecules in polymer matrices

Robust fluorescent photoswitching molecules, having perylene bisimide as the fluorescent unit and diarylethene as the switching unit, were prepared, and their photochromic reactions were measured at the single-molecule level in various polymer matrices. The histograms of the fluorescent on and off times were found to deviate from normal exponential distribution and showed a peak when the molecules are embedded in rigid polymer matrices, such as Zeonex or poly(methyl methacrylate) (PMMA). In soft polymer matrices, such as poly(n-buthyl methacrylate) (PnBMA), exponential distribution was observed for the on and off times. The abnormal distribution suggests that the quantum yields of the photoreactions are not constant and the molecules undergo the reactions after absorbing a certain number of photons. A multilocal minima model was proposed to explain the environmental effect.     

A hierarchical self-similar structure of oriented calcite with association of an agar gel matrix: inheritance of crystal habit from nanoscale

Calcite crystals grown with association of an organic gel matrix led to the generation of a hierarchical, self-similar architecture possessing rhombohedral habit under ambient conditions.     

Distribution of photo-cross-linked products from 3-aryl-3-trifluoromethyldiazirines and alcohols

The photolysis of N-[4-(3-trifluoromethyl-3H-diazirin-3-yl)benzoyl]-2,2′-ethylenedioxybis(ethylamine) (1) in EtOH, PrOH, i-PrOH, BuOH, and i-BuOH was carried out in both solution (at room temperature) and solid phase (at −196 °C), and the resultant C-H and O-H insertion products were analyzed semi-quantitatively by LC/ESI-MS/MS. The carbene insertion reactions at low temperature produced all possible C-H and O-H insertion products in a relatively uniform distribution, which could not be accomplished by the solution-phase reaction.     

Peptide Cyclization by the Use of Acylammonium Species

Although cyclic peptides have become increasingly important as drugs, the most conventional peptide cyclization method using moderately active coupling agents suffers from a lot of waste and high cost as well as long reaction times and burdensome purification. Herein, we report an unconventional approach to peptide cyclization that uses acylammonium species generated from inexpensive and less wasteful Me₂NBn and ClCO₂i-Pr. Using this approach, we observed the desired rapid activation of the C-terminus of cyclization precursors by an acylammonium ion for rapid and epimerization/dimerization-free cyclization of synthetically challenging peptides, including a difficult cyclization involving N-methyl amide bond formation. The ease of purification, productivities, and reaction mass efficiencies of our approach were significantly superior to those in previous reports. We synthesized a previously reported versicotide D analogue, and our data indicated that its assigned stereostructure should be revised.     

Asymmetric Total Synthesis of Cytotrienin A: Late-Stage Installation of C11 Side Chain onto the Macrolactam Scaffold

Cytotrienin A, an ansamycin-class antibiotic, exhibits potent apoptosis-inducing activity and has attracted much attention as a lead compound for anticancer drugs. Herein, we report a new asymmetric synthetic route to cytotrienin A, employing an unexplored approach involving the late-stage installation of a C11 side chain onto the macrolactam core. In this strategy, we utilized the redox properties of hydroquinone and installed a side chain on the sterically hindered C11 hydroxy group by the traceless Staudinger reaction. This study also demonstrated that the boron-Wittig/iterative Suzuki–Miyaura cross-coupling sequence was effective for the concise and selective construction of the (E,E,E)-conjugated triene moiety. The developed route opens new opportunities for the structure–activity relationship studies of the side chains of these ansamycin antibiotics and the preparation of other synthetic analogs and chemical probes for further biological studies.     

Approximate Bayesian Computation and Model Assessment for Repulsive Spatial Point Processes

In many applications involving spatial point patterns, we find evidence of inhibition or repulsion. The most commonly used class of models for such settings are the Gibbs point processes. A recent alternative, at least to the statistical community, is the determinantal point process. Here, we examine model fitting and inference for both of these classes of processes in a Bayesian framework. While usual MCMC model fitting can be available, the algorithms are complex and are not always well behaved. We propose using approximate Bayesian computation (ABC) for such fitting. This approach becomes attractive because, though likelihoods are very challenging to work with for these processes, generation of realizations given parameter values is relatively straightforward. As a result, the ABC fitting approach is well-suited for these models. In addition, such simulation makes them well-suited for posterior predictive inference as well as for model assessment. We provide details for all of the above along with some simulation investigation and an illustrative analysis of a point pattern of tree data exhibiting repulsion. R code and datasets are included in the supplementary material.     

A Pore-Scale Numerical Simulation Method for Estimating the Permeability of Sand Sediment

A numerical method system to estimate the permeability of sand sediments, at a microscopic scale, was developed. Initially, 3D geometrical representations of the sand grains are reconstructed from a series of 2D X-ray CT scans of real sand grains. 2D cross-sectional slices of the grain outlines are combined together to produce 3D objects via spherical harmonics series expansions. Then, the reconstructed sand grains are packed randomly inside a cubic, microscopic, domain by a combination of a growth method and a simulated annealing method to achieve a predefined porosity. Finally, a single-phase water flow within the domain was simulated numerically, using the lattice Boltzmann method. The calculated permeability of these systems compares well with the values provided by conventional theoretical models. One of the contributions of this study is to show that it is possible to predict the permeability of sand sediments of variable porosities, using sand grains from CT images with changing size distributions and orientations.     

Microscale Numerical Simulation of the Permeability Reduction due to Trapping of Suspended Fine Particles Within Sand Sediments

The reduction in permeability of sediments due to blockages caused by the trapping of suspended particles is a common concern for the extraction processes of oil or natural gas. In this study, the effect of trapped fine particles in sand sediments is studied numerically using a three-dimensional lattice Boltzmann method. The geometrical properties of larger, immobile, sand grains are digitally extracted by the spherical harmonics series expansions of CT scans of real sand grains. The migrating fine particles are assumed to be spherical in shape with their volumes following a log-normal distribution. These fine particles, together with larger frame sands, are positioned, without overlapping, within a microscopic, cubic, domain with periodic boundaries. The remaining empty volume is filled with water and imposing a pressure gradient simulates the flow of fluid through the sediment. As a result of fine particles becoming trapped by the frame sand, the initial porosity of which is 0.589, the absolute permeability of the system is reduced by approximately 60?C90?%, corresponding to fine particle saturations of 0.15?C0.29, respectively. The permeability change due to the trapping of fine particles is also modelled theoretically using not only volume saturations but also specific surface areas of both the frame sands and the fine particles with a coefficient of proportionality.