GENE FLOW AND SPECIES DELIMITATION: A CASE STUDY OF TWO PINE SPECIES WITH OVERLAPPING DISTRIBUTIONS IN SOUTHEAST CHINA

Species delimitation detected by molecular markers is complicated by introgression and incomplete lineage sorting between species. Recent modeling suggests that fixed genetic differences between species are highly related to rates of intraspecific gene flow. However, it remains unclear whether such differences are due to high levels of intraspecific gene flow overriding the spread of introgressed alleles or favoring rapid lineage sorting between species. In pines, chloroplast (cp) and mitochondrial (mt) DNAs are normally paternally and maternally inherited, respectively, and thus their relative rates of intraspecific gene flow are expected to be high and low, respectively. In this study, we used two pine species with overlapping geographical distributions in southeast China, P. massoniana and P. hwangshanensis, as a model system to examine the association between organelle gene flow and variation within and between species. We found that cpDNA variation across these two pine species is more species specific than mtDNA variation and almost delimits taxonomic boundaries. The shared mt/cp DNA genetic variation between species shows no bias in regard to parapatric versus allopatric species’ distributions. Our results therefore support the hypothesis that high intraspecific gene flow has accelerated cpDNA lineage sorting between these two pine species.     

A new strategy of transforming an ACQ compound into an AIE theranostic system for bacterial imaging and photodynamic antibacterial therapy

An organic chemical with fluorescence quenching properties [aggregation-caused quenching (ACQ)] may often be transformed by adding functional groups that cause aggregation-induced emission (AIE) to its molecular scaffold. Such structural change techniques, however, sometimes require challenging chemical reactions. SF136 is a type of chalcone, and it is an typical ACQ organic compound. In this study, cationic surfactants like hexadecyltrimethylammonium bromide (CTAB) and polyethyleneimine (PEI) were used to convert the ACQ compound SF136 into an AIE compound without adding any AIE structure units. In comparison to SF136, the SF136-CTAB NPS system not only demonstrated improved bacterial fluorescence imaging capabilities, but also increased photodynamic antibacterial activity, which is connected to its improved targeting and reactive oxygen species (ROS) production abilities. It is a promising theranostic substance against bacteria owing to these enhanced qualities. Other ACQ fluorescent compounds may also benefit from using this approach, broadening the scope of their potential applications.     

VIP Barcoding: composition vector‐based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time‐consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user‐friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two‐stage algorithm. First, an alignment‐free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment‐based K2P distance nearest‐neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment‐free methods and (ii) higher scalability than alignment‐based distance methods and character‐based methods. These results suggest that this platform is able to deal with both large‐scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/ .     

Dimethyl sulfide protects against oxidative stress and extends lifespan via a methionine sulfoxide reductase A‐dependent catalytic mechanism

Methionine (Met) sulfoxide reductase A (MsrA) is a key endogenous antioxidative enzyme with longevity benefits in animals. Only very few approaches have been reported to enhance MsrA function. Recent reports have indicated that the antioxidant capability of MsrA may involve a Met oxidase activity that facilities the reaction of Met with reactive oxygen species (ROS). Herein, we used a homology modeling approach to search the substrates for the oxidase activity of MsrA. We found that dimethyl sulfide (DMS), a main metabolite that produced by marine algae, emerged as a good substrate for MsrA‐catalytic antioxidation. MsrA bounds to DMS and promoted its antioxidant capacity via facilitating the reaction of DMS with ROS through a sulfonium intermediate at residues Cys72, Tyr103, and Glu115, followed by the release of dimethyl sulfoxide (DMSO). DMS reduced the antimycin A‐induced ROS generation in cultured PC12 cells and alleviated oxidative stress. Supplement of DMS exhibited cytoprotection and extended longevity in both Caenorhabditis elegans and Drosophila. MsrA knockdown abolished the cytoprotective effect and the longevity benefits of DMS. Furthermore, we found that the level of physiologic DMS was at the low micromolar range in different tissues of mammals and its level decreased after aging. This study opened a new window to elucidate the biological role of DMS and other low‐molecular sulfides in the cytoprotection and aging.     

Immunoelectrophoretic analysis of the antigenic structure of Sh. sonnei]

The authors studied the antigenic composition of 105 Sh. sonnei strains freshly isolated from patients suffering from acute dysentery and carriers. Immunophoregrams of pure S-and R-forms species were obtained. Up to 13 antigens differing by electrophoretic and diffusion mobility and immunological specificity were revealed among soluble Sh. sonnei antigens The position of common and specific antigens was determined on the immunophoregram. Along with the thermostable somatic O-antigen detected at the I phase of the S-forms, and two thermolabile O-antigen components at the II phase, and the R-forms, there was revealed a surface, relatively thermolabile, K-antigen of A-type capable of agglutinating live bacteria in the O-antiserum; position of the latter on the immunophoregram was also determined.     

Biodegradation of ethanethiol in aqueous medium by a new <Emphasis Type="Italic">Lysinibacillus sphaericus</Emphasis> strain RG-1 isolated from activated sludge

In the present study, a new bacterial strain isolated from activated sludge has been identified as Lysinibacillus sphaericus based on its morphology, physiochemical properties, and the results of 16S ribosomal RNA (rRNA) gene sequence analysis. This new bacterial strain uses ethanethiol as both carbon source and energy source. The key factors for controlling the degradation efficiency of ethanethiol by this strain were found to be initial ethanethiol concentration, temperature, and pH value of solutions. Under the optimized conditions, as well as 4 mg l⁻¹ ethanethiol, 30°C, and pH = 7.0, almost 100% ethanethiol can be degraded within 96 h and sulfate as a final product was detected in aqueous medium. The degradation reaction of ethanethiol over this newly isolated strain can be described by pseudo first-order equation in which the maximum degradation rate constant K and the minimum half-life were respectively calculated to be 0.0308 h⁻¹ and 22.5 h under the optimal conditions.     

Polyoma-like Virions in Human Demyelinating Brain Disease

Specimens of brain tissue obtained at autopsy from three patients suffering from progressive multifocal leukoencephalopathy (PML) were examined by electron microscopy. In specimens from all three cases particles similar to those of the papova virus group were present, confirming previous observations. By the negative staining method it was possible to define the morphological characteristics of the particles more precisely and it was shown that they are structurally similar to virions of the polyoma-SV40-K type. The need is emphasized for obtaining fresh unfixed diseased tissue from persons suffering from PML in order that the biological properties of the particles can be investigated.