Genetic Diversity and Population Structure of Spirobolus bungii as Revealed by Mitochondrial DNA Sequences.

Soil macrofauna, such as Spirobolus bungii, are an important component of ecosystems. However, systematic studies of the genetic diversity, population genetic structure, and the potential factors affecting the genetic differentiation of S. bungii are lacking. We performed a population genetic study of 166 individuals from the mountains to the south of the Yangtze River, north of the Yangtze River in Nanjing city, and near Tianjin city, in order to investigate the correlations between geographical distance and genetic diversity. A total of 1182 bp of COX2 and Cytb gene sequences of mitochondrial DNA, and 700 bp of the 18S rRNA gene sequence were analyzed. There were two haplotypes and one variable site in the 18S rRNA gene, and 28 haplotypes and 78 variable sites in the COX2 and Cytb genes. In this study, the 18S rRNA gene was used for species identification, and mtDNA (concatenated sequences with Cytb and COX2) was used for population genetic analysis. Structure cluster analysis indicated that the genetic structures of the different populations of S. bungii tended to be consistent at small geographical scales. Phylogenetic trees revealed that the haplotypes were clearly divided into three branches: the area south of the Yangtze River, the area to the north of the Yangtze River in Nanjing, and the area in Tianjin. Large geographical barriers and long geographical distance significantly blocked gene flow between populations of S. bungii. Our results provide a basic theoretical basis for subsequent studies of millipede taxonomy and population genetic evolution.

Comparative mitogenomes of three species in Moenkhausia: Rare irregular gene rearrangement within Characidae.

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangements. However, a new type of gene arrangement has been identified in the mitochondrial genomes (mitogenomes) of Moenkhausia. Here, three newly sequenced complete mitogenomes of tetras (Characidae: Moenkhausia) are presented (M. costae, M. pittieri, and M. sanctaefilomenae). The three mitogenomes had a classical circular structure, with total lengths ranging from 15,811 to 18,435 bp. Base composition analysis indicated that the sequences were biased toward adenine (A) and thymine (T), with A + T content of 54.63% in M. costae, 58.47% in M. pittieri, and 59.98% in M. sanctaefilomenae. The gene order and organization of M. sanctaefilomenae differed from those of typical teleostean mitogenomes. The genes tRNA-Ile, tRNA-Gln, and tRNA-Pro were translocated between tRNA-Trp and tRNA-Asn. One extra tRNA-Met and an extra CR were also discovered in the mitogenome. BI and ML analyses based on sequences of 38 different mitogenomes showed that M. costae and M. pittieri were classified together, and M. sanctaefilomenae was slightly further from other fish of the same genus. These results provide insight into the gene arrangement features of Characidae mitogenomes and lay the foundation for further phylogenetic studies on Characidae.

A near-infrared fluorescent probe for evaluating endogenous hydrogen peroxide during ischemia/reperfusion injury.

Hydrogen peroxide (H2O2), as a major component of reactive oxygen species (ROS), plays an important role in normal physiological processes. A H2O2 burst also occurs in the ischemia/reperfusion (I/R) process and causes a series of physiological and pathological injuries. Therefore, it is important to determine concentration fluctuations of H2O2. Here we develop a ratiometric fluorescent probe, Cy-ArB, which shows high selectivity and sensitivity toward H2O2. The fluorescence response of the probe is triggered by the reaction of borate esters with H2O2, and this process releases a near-infrared heptamethine cyanine fluorophore which has the ability of mitochondrial tracing. Hence, the probe can be used for real-time monitoring of H2O2 fluctuations in the mitochondrial respiration chain. Finally, we explore the fluctuations of H2O2 in cells and in vivo during the I/R process using the probe Cy-ArB. The results of our experiments prove that our probe is a potential candidate for clinical surgery pre-evaluation.

Theoretical study of the spectroscopic and nonlinear optical properties of trans- and cis-4-hydroxyazobenzene.

We investigate the molecular structure, vibrational and electronic absorption spectra, and electronic hyperpolarizabilities of trans and cis isomers of 4-hydroxyazobenzene (HOAB) via density functional theory. Results show that the azo dye exhibits a high third-order nonlinear optical response and good optical transparency. Both the basis set and the functional are important influences on the results obtained when calculating the absorption spectrum and NLO response. We also study the effect of the solvent on the electronic absorption spectrum to assess the ability of the functional to reproduce the experimental spectrum in combination with a suitable solvent model. Our calculations show that the SMD model of Truhlar et al. handles the electrostatic and the non-electrostatic effects of hydrogen-bonding solvents on the absorption spectrum better than the traditional polarizable continuum model does. In addition, our results indicate that the dye trans-HOAB exhibits a high second hyperpolarizability and excellent optical transparency. Also, although the second hyperpolarizability of cis-HOAB is much lower than that of trans-HOAB, it is non-negligible when calculating the optical nonlinearity of HOAB under an optical pump. We also examine the effect of frequency dispersion on second harmonic generation. This study provides the basis for further research on the spectroscopic and nonlinear optical properties of novel azo dyes and other π-conjugated compounds.

Size-, electric-field-, and frequency-dependent third-order nonlinear optical properties of hydrogenated silicon nanoclusters.

We investigated the electronic properties and second hyperpolarizabilities of hydrogenated silicon nanoclusters (H-SiNCs) by using the density functional theory method. The effects of cluster size, external electric field and incident frequency on the second hyperpolarizability were also examined, respectively. We found that small H-SiNCs exhibit large second hyperpolarizability. With the increase of the number of silicon atoms in H-SiNCs, the frontier molecular orbital energy gap decreases, attributed to the enhancement of the second hyperpolarizability. Interestingly, we also found the electric-field-induced gigantic enhancement of the second hyperpolarizability for H-SiNCs due to the change of electron density distributions. In addition, our results demonstrate a significant dependence on the frequency of incident light.